--- /dev/null
+HEADER OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ \r
+ATOM 2 CA GLU A 19 20.491 30.713 36.290 1.00 74.29 C \r
+ATOM 11 CA SER A 20 24.056 29.774 37.264 1.00 72.09 C \r
+ATOM 17 CA LYS A 21 27.517 31.289 37.563 1.00 70.09 C \r
+ATOM 26 CA LYS A 22 28.794 27.865 36.481 1.00 68.64 C \r
+ATOM 35 CA GLN A 23 29.484 26.806 32.884 1.00 70.46 C \r
+ATOM 44 CA GLU A 24 26.420 25.175 31.360 1.00 72.08 C \r
+ATOM 53 CA GLU A 25 26.736 26.049 27.683 1.00 70.43 C \r
+ATOM 62 CA GLY A 26 28.299 22.912 26.233 1.00 63.14 C \r
+ATOM 66 CA VAL A 27 26.863 20.704 28.982 1.00 54.50 C \r
+ATOM 73 CA VAL A 28 25.030 17.390 28.655 1.00 48.32 C \r
+ATOM 80 CA THR A 29 23.728 14.677 30.991 1.00 44.86 C \r
+ATOM 87 CA ASN A 30 22.327 11.164 30.703 1.00 45.42 C \r
+ATOM 95 CA LEU A 31 23.332 10.459 27.102 1.00 45.42 C \r
+ATOM 103 CA TYR A 32 23.549 6.898 28.380 1.00 45.88 C \r
+ATOM 115 CA LYS A 33 21.656 5.321 31.262 1.00 47.27 C \r
+ATOM 124 CA PRO A 34 21.991 2.046 33.248 1.00 48.99 C \r
+ATOM 131 CA LYS A 35 19.339 0.560 30.970 1.00 52.75 C \r
+ATOM 140 CA GLU A 36 21.580 0.855 27.886 1.00 53.33 C \r
+ATOM 149 CA PRO A 37 25.154 2.015 28.678 1.00 47.54 C \r
+ATOM 156 CA TYR A 38 27.929 2.872 26.249 1.00 41.98 C \r
+ATOM 168 CA VAL A 39 30.355 -0.017 25.909 1.00 41.48 C \r
+ATOM 175 CA GLY A 40 33.823 1.485 25.966 1.00 37.59 C \r
+ATOM 179 CA ARG A 41 37.165 -0.277 26.122 1.00 39.77 C \r
+ATOM 190 CA CYS A 42 40.148 -0.029 28.442 1.00 36.51 C \r
+ATOM 196 CA LEU A 43 43.095 1.441 26.554 1.00 36.13 C \r
+ATOM 204 CA LEU A 44 45.231 2.023 29.649 1.00 33.55 C \r
+ATOM 212 CA ASN A 45 45.140 1.026 33.307 1.00 27.79 C \r
+ATOM 220 CA THR A 46 48.056 1.800 35.617 1.00 28.75 C \r
+ATOM 227 CA LYS A 47 48.542 1.776 39.388 1.00 30.31 C \r
+ATOM 236 CA ILE A 48 49.564 5.317 40.376 1.00 31.32 C \r
+ATOM 244 CA THR A 49 50.339 4.682 44.059 1.00 37.62 C \r
+ATOM 251 CA GLY A 50 53.585 3.317 45.460 1.00 44.49 C \r
+ATOM 255 CA ASP A 51 53.706 -0.448 46.087 1.00 52.89 C \r
+ATOM 263 CA ASP A 52 53.910 0.545 49.751 1.00 55.23 C \r
+ATOM 271 CA ALA A 53 50.816 2.767 50.056 1.00 53.34 C \r
+ATOM 276 CA PRO A 54 47.904 1.940 52.405 1.00 50.60 C \r
+ATOM 283 CA GLY A 55 45.420 1.579 49.561 1.00 50.35 C \r
+ATOM 287 CA GLU A 56 46.098 1.286 45.836 1.00 42.53 C \r
+ATOM 296 CA THR A 57 44.534 3.816 43.480 1.00 41.14 C \r
+ATOM 303 CA TRP A 58 44.540 3.423 39.708 1.00 35.60 C \r
+ATOM 317 CA HIS A 59 44.468 5.853 36.796 1.00 31.89 C \r
+ATOM 327 CA MET A 60 42.658 4.227 33.866 1.00 31.65 C \r
+ATOM 335 CA VAL A 61 41.716 5.345 30.350 1.00 30.43 C \r
+ATOM 342 CA PHE A 62 38.669 4.172 28.360 1.00 34.36 C \r
+ATOM 353 CA SER A 63 37.657 4.908 24.772 1.00 34.69 C \r
+ATOM 359 CA THR A 64 34.448 6.828 23.951 1.00 36.96 C \r
+ATOM 366 CA GLU A 65 34.691 7.644 20.254 1.00 40.08 C \r
+ATOM 375 CA GLY A 66 33.742 11.183 21.285 1.00 40.22 C \r
+ATOM 379 CA LYS A 67 30.272 9.763 22.003 1.00 41.93 C \r
+ATOM 388 CA ILE A 68 30.279 11.116 25.577 1.00 41.52 C \r
+ATOM 396 CA PRO A 69 30.791 14.926 25.537 1.00 42.35 C \r
+ATOM 403 CA TYR A 70 31.228 15.232 29.299 1.00 39.84 C \r
+ATOM 415 CA ARG A 71 32.639 18.451 30.768 1.00 44.14 C \r
+ATOM 426 CA GLU A 72 35.122 19.278 33.515 1.00 43.82 C \r
+ATOM 435 CA GLY A 73 33.472 18.458 36.835 1.00 41.97 C \r
+ATOM 439 CA GLN A 74 30.929 15.874 35.657 1.00 37.19 C \r
+ATOM 448 CA SER A 75 31.285 12.124 36.138 1.00 38.28 C \r
+ATOM 454 CA ILE A 76 30.458 8.792 34.539 1.00 36.84 C \r
+ATOM 462 CA GLY A 77 28.983 5.620 35.918 1.00 35.39 C \r
+ATOM 466 CA VAL A 78 30.311 2.108 35.530 1.00 32.05 C \r
+ATOM 473 CA ILE A 79 28.458 -1.201 35.591 1.00 32.67 C \r
+ATOM 481 CA ALA A 80 30.745 -4.018 36.644 1.00 35.36 C \r
+ATOM 486 CA ASP A 81 30.359 -7.373 34.872 1.00 38.72 C \r
+ATOM 494 CA GLY A 82 28.308 -10.332 36.110 1.00 45.79 C \r
+ATOM 498 CA VAL A 83 25.820 -10.242 39.001 1.00 52.24 C \r
+ATOM 505 CA ASP A 84 25.838 -10.250 42.834 1.00 60.54 C \r
+ATOM 513 CA LYS A 85 25.014 -13.158 45.196 1.00 66.72 C \r
+ATOM 522 CA ASN A 86 21.414 -13.062 43.904 1.00 67.37 C \r
+ATOM 530 CA GLY A 87 21.724 -13.423 40.136 1.00 64.74 C \r
+ATOM 534 CA LYS A 88 20.971 -9.733 39.570 1.00 61.12 C \r
+ATOM 543 CA PRO A 89 23.054 -7.201 37.561 1.00 54.68 C \r
+ATOM 550 CA HIS A 90 25.224 -4.957 39.755 1.00 44.44 C \r
+ATOM 560 CA LYS A 91 23.940 -1.433 40.260 1.00 40.48 C \r
+ATOM 569 CA VAL A 92 25.803 1.546 38.843 1.00 38.45 C \r
+ATOM 576 CA ARG A 93 28.709 2.986 40.828 1.00 38.93 C \r
+ATOM 587 CA LEU A 94 29.778 6.584 40.096 1.00 34.37 C \r
+ATOM 595 CA TYR A 95 33.309 7.878 39.513 1.00 30.27 C \r
+ATOM 607 CA SER A 96 34.425 11.475 39.057 1.00 29.44 C \r
+ATOM 613 CA ILE A 97 36.029 12.090 35.662 1.00 27.61 C \r
+ATOM 621 CA ALA A 98 39.769 12.693 36.069 1.00 31.12 C \r
+ATOM 626 CA SER A 99 40.393 13.712 32.475 1.00 32.42 C \r
+ATOM 632 CA SER A 100 39.566 17.142 31.059 1.00 36.14 C \r
+ATOM 638 CA ALA A 101 37.097 17.367 28.154 1.00 41.07 C \r
+ATOM 643 CA ILE A 102 39.764 16.549 25.527 1.00 47.65 C \r
+ATOM 651 CA GLY A 103 41.172 13.692 27.599 1.00 46.77 C \r
+ATOM 655 CA ASP A 104 44.730 12.612 28.289 1.00 43.82 C \r
+ATOM 663 CA PHE A 105 45.115 12.065 24.522 1.00 41.52 C \r
+ATOM 674 CA GLY A 106 43.862 15.455 23.328 1.00 41.66 C \r
+ATOM 678 CA ASP A 107 41.355 13.883 20.926 1.00 40.90 C \r
+ATOM 686 CA SER A 108 38.132 14.250 22.954 1.00 42.95 C \r
+ATOM 692 CA LYS A 109 37.967 10.535 22.224 1.00 44.74 C \r
+ATOM 701 CA THR A 110 38.731 9.184 25.704 1.00 41.09 C \r
+ATOM 708 CA VAL A 111 37.728 9.519 29.374 1.00 39.03 C \r
+ATOM 715 CA SER A 112 39.912 8.705 32.399 1.00 37.17 C \r
+ATOM 721 CA LEU A 113 39.098 7.476 35.935 1.00 32.10 C \r
+ATOM 729 CA CYS A 114 40.964 7.578 39.261 1.00 30.65 C \r
+ATOM 735 CA VAL A 115 39.724 4.459 41.060 1.00 33.45 C \r
+ATOM 742 CA LYS A 116 40.668 3.524 44.628 1.00 34.75 C \r
+ATOM 751 CA ARG A 117 40.376 -0.250 45.123 1.00 32.85 C \r
+ATOM 762 CA LEU A 118 38.137 -1.094 48.077 1.00 30.50 C \r
+ATOM 770 CA ILE A 119 39.376 -3.752 50.459 1.00 34.34 C \r
+ATOM 778 CA TYR A 120 38.699 -4.266 54.125 1.00 31.39 C \r
+ATOM 790 CA THR A 121 38.264 -7.086 56.567 1.00 28.83 C \r
+ATOM 797 CA ASN A 122 34.792 -7.477 58.109 1.00 26.51 C \r
+ATOM 805 CA ASP A 123 33.626 -8.382 61.634 1.00 31.58 C \r
+ATOM 813 CA ALA A 124 34.191 -12.077 60.901 1.00 27.84 C \r
+ATOM 818 CA GLY A 125 37.759 -11.844 59.728 1.00 32.39 C \r
+ATOM 822 CA GLU A 126 36.809 -12.146 56.073 1.00 35.82 C \r
+ATOM 831 CA ILE A 127 38.655 -9.932 53.598 1.00 38.42 C \r
+ATOM 839 CA VAL A 128 36.025 -8.261 51.421 1.00 33.73 C \r
+ATOM 846 CA LYS A 129 36.482 -6.484 48.090 1.00 31.87 C \r
+ATOM 855 CA GLY A 130 34.363 -3.680 46.686 1.00 26.91 C \r
+ATOM 859 CA VAL A 131 32.680 -5.051 43.569 1.00 27.89 C \r
+ATOM 866 CA CYS A 132 33.074 -2.246 41.018 1.00 28.46 C \r
+ATOM 872 CA SER A 133 36.266 -0.553 42.213 1.00 31.33 C \r
+ATOM 878 CA ASN A 134 37.861 -3.983 41.984 1.00 30.29 C \r
+ATOM 886 CA PHE A 135 36.318 -4.795 38.623 1.00 31.48 C \r
+ATOM 897 CA LEU A 136 37.926 -1.553 37.520 1.00 27.81 C \r
+ATOM 905 CA CYS A 137 41.417 -1.976 38.955 1.00 25.91 C \r
+ATOM 911 CA ASP A 138 41.605 -5.419 37.338 1.00 30.22 C \r
+ATOM 919 CA LEU A 139 40.462 -4.306 33.874 1.00 32.69 C \r
+ATOM 927 CA GLN A 140 42.851 -5.511 31.186 1.00 36.80 C \r
+ATOM 936 CA PRO A 141 43.380 -3.220 28.170 1.00 36.16 C \r
+ATOM 943 CA GLY A 142 40.864 -4.420 25.586 1.00 31.10 C \r
+ATOM 947 CA ASP A 143 38.129 -5.298 28.055 1.00 30.62 C \r
+ATOM 955 CA ASN A 144 34.690 -3.847 27.645 1.00 33.52 C \r
+ATOM 963 CA VAL A 145 33.430 -1.522 30.361 1.00 37.08 C \r
+ATOM 970 CA GLN A 146 29.817 -0.374 30.523 1.00 37.65 C \r
+ATOM 979 CA ILE A 147 29.547 3.413 31.045 1.00 30.95 C \r
+ATOM 987 CA THR A 148 26.637 5.791 31.832 1.00 29.95 C \r
+ATOM 994 CA GLY A 149 26.297 9.581 31.843 1.00 32.81 C \r
+ATOM 998 CA PRO A 150 27.785 12.148 31.800 1.00 34.98 C \r
+ATOM 1005 CA VAL A 151 26.376 12.668 35.275 1.00 36.53 C \r
+ATOM 1012 CA GLY A 152 26.196 15.756 37.474 1.00 43.09 C \r
+ATOM 1016 CA LYS A 153 26.048 19.528 37.068 1.00 48.37 C \r
+ATOM 1025 CA GLU A 154 26.921 20.540 40.633 1.00 49.70 C \r
+ATOM 1034 CA MET A 155 30.710 20.266 40.235 1.00 47.30 C \r
+ATOM 1042 CA LEU A 156 30.882 22.020 36.869 1.00 50.36 C \r
+ATOM 1050 CA MET A 157 33.362 24.883 36.404 1.00 55.29 C \r
+ATOM 1058 CA PRO A 158 32.521 28.612 36.605 1.00 54.88 C \r
+ATOM 1065 CA LYS A 159 32.291 30.776 33.464 1.00 54.92 C \r
+ATOM 1074 CA ASP A 160 34.497 33.503 34.939 1.00 57.22 C \r
+ATOM 1082 CA PRO A 161 38.055 32.687 33.759 1.00 58.62 C \r
+ATOM 1089 CA ASN A 162 39.524 35.240 36.163 1.00 60.44 C \r
+ATOM 1097 CA ALA A 163 37.814 33.910 39.279 1.00 55.80 C \r
+ATOM 1102 CA THR A 164 39.596 32.487 42.316 1.00 51.04 C \r
+ATOM 1109 CA ILE A 165 38.966 28.771 42.756 1.00 50.26 C \r
+ATOM 1117 CA ILE A 166 39.774 26.773 45.885 1.00 47.54 C \r
+ATOM 1125 CA MET A 167 39.883 23.014 45.324 1.00 46.38 C \r
+ATOM 1133 CA LEU A 168 39.700 20.963 48.522 1.00 42.18 C \r
+ATOM 1141 CA ALA A 169 40.377 17.316 47.770 1.00 36.41 C \r
+ATOM 1146 CA THR A 170 41.005 14.086 49.622 1.00 32.98 C \r
+ATOM 1153 CA GLY A 171 42.027 10.802 48.014 1.00 31.36 C \r
+ATOM 1157 CA THR A 172 40.386 10.037 44.680 1.00 30.48 C \r
+ATOM 1164 CA GLY A 173 38.640 13.335 45.359 1.00 33.99 C \r
+ATOM 1168 CA ILE A 174 41.418 15.036 43.394 1.00 35.66 C \r
+ATOM 1176 CA ALA A 175 39.758 13.585 40.300 1.00 36.00 C \r
+ATOM 1181 CA PRO A 176 37.445 16.385 39.155 1.00 39.41 C \r
+ATOM 1188 CA PHE A 177 40.109 18.971 39.976 1.00 43.21 C \r
+ATOM 1199 CA ARG A 178 42.726 17.119 37.955 1.00 41.09 C \r
+ATOM 1210 CA SER A 179 40.235 17.536 35.124 1.00 39.92 C \r
+ATOM 1216 CA PHE A 180 39.808 21.204 36.009 1.00 39.23 C \r
+ATOM 1227 CA LEU A 181 43.528 21.949 35.995 1.00 39.50 C \r
+ATOM 1235 CA TRP A 182 44.305 20.081 32.770 1.00 41.47 C \r
+ATOM 1249 CA LYS A 183 42.141 22.654 30.972 1.00 48.08 C \r
+ATOM 1258 CA MET A 184 43.477 25.547 33.062 1.00 52.79 C \r
+ATOM 1266 CA PHE A 185 47.102 25.043 32.014 1.00 57.35 C \r
+ATOM 1277 CA PHE A 186 48.075 21.921 30.051 1.00 55.98 C \r
+ATOM 1288 CA GLU A 187 45.758 23.173 27.297 1.00 54.44 C \r
+ATOM 1297 CA LYS A 188 44.908 26.236 25.196 1.00 51.29 C \r
+ATOM 1306 CA HIS A 189 41.395 27.080 24.003 1.00 51.35 C \r
+ATOM 1316 CA ASP A 190 40.108 29.972 21.873 1.00 54.30 C \r
+ATOM 1324 CA ASP A 191 37.199 30.481 24.249 1.00 53.95 C \r
+ATOM 1332 CA TYR A 192 38.816 29.937 27.634 1.00 50.68 C \r
+ATOM 1344 CA LYS A 193 41.916 31.388 29.230 1.00 51.00 C \r
+ATOM 1353 CA PHE A 194 42.322 30.967 32.956 1.00 52.09 C \r
+ATOM 1364 CA ASN A 195 43.672 34.234 34.312 1.00 56.46 C \r
+ATOM 1372 CA GLY A 196 42.616 34.078 37.969 1.00 57.17 C \r
+ATOM 1376 CA LEU A 197 43.874 31.920 40.843 1.00 57.92 C \r
+ATOM 1384 CA GLY A 198 43.549 28.151 41.086 1.00 56.67 C \r
+ATOM 1388 CA TRP A 199 44.258 26.886 44.592 1.00 51.55 C \r
+ATOM 1402 CA LEU A 200 44.411 23.170 45.379 1.00 49.17 C \r
+ATOM 1410 CA PHE A 201 44.558 21.335 48.709 1.00 48.60 C \r
+ATOM 1421 CA LEU A 202 45.122 17.570 48.598 1.00 45.34 C \r
+ATOM 1429 CA GLY A 203 44.885 15.480 51.742 1.00 48.55 C \r
+ATOM 1433 CA VAL A 204 46.225 11.936 51.755 1.00 50.23 C \r
+ATOM 1440 CA PRO A 205 47.942 9.740 54.365 1.00 51.51 C \r
+ATOM 1447 CA THR A 206 51.284 9.148 52.648 1.00 50.21 C \r
+ATOM 1454 CA SER A 207 53.551 10.483 49.894 1.00 49.38 C \r
+ATOM 1460 CA SER A 208 53.267 7.061 48.259 1.00 43.49 C \r
+ATOM 1466 CA SER A 209 49.588 8.049 48.093 1.00 42.57 C \r
+ATOM 1472 CA LEU A 210 49.990 11.424 46.364 1.00 42.65 C \r
+ATOM 1480 CA LEU A 211 48.121 11.446 43.035 1.00 39.33 C \r
+ATOM 1488 CA TYR A 212 49.516 13.214 39.935 1.00 40.89 C \r
+ATOM 1500 CA LYS A 213 52.128 15.234 41.873 1.00 45.88 C \r
+ATOM 1509 CA GLU A 214 54.518 15.406 38.899 1.00 53.22 C \r
+ATOM 1518 CA GLU A 215 51.680 16.911 36.889 1.00 55.16 C \r
+ATOM 1527 CA PHE A 216 50.757 19.475 39.514 1.00 60.55 C \r
+ATOM 1538 CA GLY A 217 54.488 20.153 39.524 1.00 66.64 C \r
+ATOM 1542 CA LYS A 218 54.575 21.110 35.850 1.00 68.86 C \r
+ATOM 1551 CA MET A 219 51.398 23.159 36.265 1.00 66.97 C \r
+ATOM 1559 CA LYS A 220 53.138 25.090 39.061 1.00 65.97 C \r
+ATOM 1568 CA GLU A 221 55.654 26.250 36.459 1.00 70.02 C \r
+ATOM 1577 CA ARG A 222 53.584 26.507 33.294 1.00 73.48 C \r
+ATOM 1588 CA ALA A 223 52.005 29.449 35.175 1.00 76.21 C \r
+ATOM 1593 CA PRO A 224 53.272 29.877 38.804 1.00 79.25 C \r
+ATOM 1600 CA GLU A 225 51.296 33.124 39.020 1.00 81.84 C \r
+ATOM 1609 CA ASN A 226 47.873 31.528 38.622 1.00 78.84 C \r
+ATOM 1617 CA PHE A 227 48.418 28.176 40.350 1.00 75.28 C \r
+ATOM 1628 CA ARG A 228 49.090 27.305 43.996 1.00 72.05 C \r
+ATOM 1639 CA VAL A 229 49.165 23.724 45.323 1.00 68.82 C \r
+ATOM 1646 CA ASP A 230 49.258 22.581 48.958 1.00 66.54 C \r
+ATOM 1654 CA TYR A 231 49.605 18.943 49.968 1.00 60.31 C \r
+ATOM 1666 CA ALA A 232 48.551 17.560 53.332 1.00 57.39 C \r
+ATOM 1671 CA VAL A 233 50.260 14.228 53.945 1.00 57.14 C \r
+ATOM 1678 CA SER A 234 48.465 13.579 57.244 1.00 60.81 C \r
+ATOM 1684 CA ARG A 235 50.959 11.010 58.514 1.00 60.74 C \r
+ATOM 1695 CA GLU A 236 54.268 12.594 57.481 1.00 59.17 C \r
+ATOM 1704 CA GLN A 237 53.494 16.197 58.450 1.00 59.62 C \r
+ATOM 1713 CA THR A 238 52.590 18.236 61.521 1.00 63.18 C \r
+ATOM 1720 CA ASN A 239 52.019 21.937 62.188 1.00 66.71 C \r
+ATOM 1728 CA ALA A 240 52.096 23.767 65.537 1.00 70.06 C \r
+ATOM 1733 CA ALA A 241 51.302 21.400 68.410 1.00 72.44 C \r
+ATOM 1738 CA GLY A 242 52.383 18.324 66.438 1.00 72.38 C \r
+ATOM 1742 CA GLU A 243 48.826 18.169 65.110 1.00 69.71 C \r
+ATOM 1751 CA ARG A 244 48.674 15.776 62.148 1.00 67.21 C \r
+ATOM 1762 CA MET A 245 48.712 17.796 58.933 1.00 64.20 C \r
+ATOM 1770 CA TYR A 246 45.246 17.082 57.556 1.00 60.65 C \r
+ATOM 1782 CA ILE A 247 43.617 18.437 54.409 1.00 62.98 C \r
+ATOM 1790 CA GLN A 248 42.035 21.001 56.761 1.00 64.64 C \r
+ATOM 1799 CA THR A 249 45.057 21.461 59.009 1.00 63.37 C \r
+ATOM 1806 CA ARG A 250 46.891 22.664 55.903 1.00 62.47 C \r
+ATOM 1817 CA MET A 251 44.123 25.201 55.251 1.00 63.35 C \r
+ATOM 1825 CA ALA A 252 44.571 26.305 58.854 1.00 65.73 C \r
+ATOM 1830 CA GLU A 253 47.973 27.809 58.076 1.00 65.97 C \r
+ATOM 1839 CA TYR A 254 46.267 30.063 55.517 1.00 65.83 C \r
+ATOM 1851 CA LYS A 255 42.991 30.559 57.379 1.00 70.30 C \r
+ATOM 1860 CA GLU A 256 43.578 34.326 57.320 1.00 73.73 C \r
+ATOM 1869 CA GLU A 257 44.189 34.738 53.593 1.00 71.52 C \r
+ATOM 1878 CA LEU A 258 41.459 32.202 52.893 1.00 73.38 C \r
+ATOM 1886 CA TRP A 259 38.790 34.074 54.853 1.00 76.72 C \r
+ATOM 1900 CA GLU A 260 39.721 37.275 53.006 1.00 78.61 C \r
+ATOM 1909 CA LEU A 261 38.580 35.553 49.815 1.00 75.71 C \r
+ATOM 1917 CA LEU A 262 35.391 33.881 51.047 1.00 73.74 C \r
+ATOM 1925 CA LYS A 263 33.562 37.165 50.535 1.00 73.64 C \r
+ATOM 1934 CA LYS A 264 34.299 38.143 46.954 1.00 72.48 C \r
+ATOM 1943 CA ASP A 265 31.954 37.554 43.993 1.00 69.65 C \r
+ATOM 1951 CA ASN A 266 34.660 35.649 42.106 1.00 65.06 C \r
+ATOM 1959 CA THR A 267 35.835 33.117 44.683 1.00 58.24 C \r
+ATOM 1966 CA TYR A 268 34.459 29.646 43.909 1.00 51.04 C \r
+ATOM 1978 CA VAL A 269 35.192 26.827 46.382 1.00 44.95 C \r
+ATOM 1985 CA TYR A 270 35.012 23.150 45.368 1.00 44.96 C \r
+ATOM 1997 CA MET A 271 35.162 20.122 47.656 1.00 41.72 C \r
+ATOM 2005 CA CYS A 272 35.314 16.468 46.632 1.00 37.19 C \r
+ATOM 2011 CA GLY A 273 36.343 13.080 47.951 1.00 37.65 C \r
+ATOM 2015 CA LEU A 274 36.040 10.886 51.020 1.00 39.39 C \r
+ATOM 2023 CA LYS A 275 33.076 12.283 52.955 1.00 44.86 C \r
+ATOM 2032 CA GLY A 276 34.322 13.183 56.400 1.00 49.16 C \r
+ATOM 2036 CA MET A 277 36.932 15.608 55.168 1.00 53.30 C \r
+ATOM 2044 CA GLU A 278 33.917 17.921 55.165 1.00 56.74 C \r
+ATOM 2053 CA LYS A 279 33.531 18.089 58.947 1.00 59.30 C \r
+ATOM 2062 CA GLY A 280 36.982 19.413 59.776 1.00 58.94 C \r
+ATOM 2066 CA ILE A 281 36.705 22.048 57.063 1.00 61.43 C \r
+ATOM 2074 CA ASP A 282 33.453 23.402 58.515 1.00 67.06 C \r
+ATOM 2082 CA ASP A 283 35.050 23.189 61.972 1.00 74.12 C \r
+ATOM 2090 CA ILE A 284 37.991 25.422 61.040 1.00 78.49 C \r
+ATOM 2098 CA MET A 285 35.456 27.566 59.201 1.00 82.25 C \r
+ATOM 2106 CA VAL A 286 32.941 27.959 62.027 1.00 83.44 C \r
+ATOM 2113 CA SER A 287 35.610 29.113 64.469 1.00 83.43 C \r
+ATOM 2119 CA LEU A 288 36.927 31.601 61.887 1.00 85.53 C \r
+ATOM 2127 CA ALA A 289 33.506 33.025 60.970 1.00 86.85 C \r
+ATOM 2132 CA GLU A 290 31.841 32.696 64.387 1.00 89.26 C \r
+ATOM 2141 CA LYS A 291 34.438 35.312 65.347 1.00 88.73 C \r
+ATOM 2150 CA ASP A 292 33.635 37.891 62.652 1.00 88.03 C \r
+ATOM 2158 CA GLY A 293 30.219 37.450 61.081 1.00 87.88 C \r
+ATOM 2162 CA ILE A 294 27.319 35.051 61.511 1.00 84.61 C \r
+ATOM 2170 CA ASP A 295 27.665 31.329 62.188 1.00 82.45 C \r
+ATOM 2178 CA TRP A 296 29.539 29.627 59.355 1.00 80.12 C \r
+ATOM 2192 CA PHE A 297 26.527 27.452 58.512 1.00 78.99 C \r
+ATOM 2203 CA ASP A 298 24.167 30.241 57.486 1.00 76.37 C \r
+ATOM 2211 CA TYR A 299 27.074 31.748 55.561 1.00 74.07 C \r
+ATOM 2223 CA LYS A 300 27.679 28.620 53.473 1.00 74.31 C \r
+ATOM 2232 CA LYS A 301 24.059 29.146 52.464 1.00 75.97 C \r
+ATOM 2241 CA GLN A 302 24.921 32.563 51.018 1.00 75.38 C \r
+ATOM 2250 CA LEU A 303 27.896 31.099 49.155 1.00 72.10 C \r
+ATOM 2258 CA LYS A 304 25.917 28.207 47.690 1.00 72.08 C \r
+ATOM 2267 CA ARG A 305 23.595 31.021 46.594 1.00 74.82 C \r
+ATOM 2278 CA GLY A 306 26.071 32.136 43.958 1.00 71.84 C \r
+ATOM 2282 CA ASP A 307 27.505 28.682 43.220 1.00 67.23 C \r
+ATOM 2290 CA GLN A 308 30.620 29.291 45.346 1.00 60.18 C \r
+ATOM 2299 CA TRP A 309 30.585 26.177 47.537 1.00 52.25 C \r
+ATOM 2313 CA ASN A 310 29.894 22.997 45.597 1.00 45.03 C \r
+ATOM 2321 CA VAL A 311 30.327 19.716 47.403 1.00 39.13 C \r
+ATOM 2328 CA GLU A 312 30.507 16.190 46.110 1.00 35.17 C \r
+ATOM 2337 CA VAL A 313 31.761 13.957 48.861 1.00 30.12 C \r
+ATOM 2344 CA TYR A 314 31.112 10.230 49.021 1.00 28.23 C \r
+ATOM 2358 CA ALA B 1 2.311 24.702 44.475 1.00 74.17 C \r
+ATOM 2363 CA THR B 2 3.590 24.207 48.055 1.00 74.76 C \r
+ATOM 2370 CA TYR B 3 3.069 20.876 49.837 1.00 73.52 C \r
+ATOM 2382 CA ASN B 4 3.748 19.874 53.435 1.00 75.75 C \r
+ATOM 2390 CA VAL B 5 6.618 17.399 53.868 1.00 75.95 C \r
+ATOM 2397 CA LYS B 6 7.769 15.523 56.983 1.00 77.70 C \r
+ATOM 2406 CA LEU B 7 11.351 14.325 57.458 1.00 78.91 C \r
+ATOM 2414 CA ILE B 8 11.807 11.511 59.985 1.00 81.00 C \r
+ATOM 2422 CA THR B 9 15.560 12.046 60.247 1.00 87.49 C \r
+ATOM 2429 CA PRO B 10 17.662 9.793 62.539 1.00 92.94 C \r
+ATOM 2436 CA GLU B 11 18.161 13.147 64.282 1.00 96.61 C \r
+ATOM 2445 CA GLY B 12 14.579 14.154 65.041 1.00 97.52 C \r
+ATOM 2449 CA GLU B 13 11.602 14.823 62.748 1.00 96.90 C \r
+ATOM 2458 CA VAL B 14 11.547 17.892 60.480 1.00 96.63 C \r
+ATOM 2465 CA GLU B 15 8.340 19.701 59.440 1.00 94.86 C \r
+ATOM 2474 CA LEU B 16 9.471 21.479 56.254 1.00 91.55 C \r
+ATOM 2482 CA GLN B 17 7.281 23.141 53.598 1.00 89.75 C \r
+ATOM 2491 CA VAL B 18 8.485 22.069 50.145 1.00 87.92 C \r
+ATOM 2498 CA PRO B 19 6.906 23.558 46.964 1.00 86.35 C \r
+ATOM 2505 CA ASP B 20 5.990 21.744 43.717 1.00 86.29 C \r
+ATOM 2513 CA ASP B 21 8.578 22.751 41.083 1.00 83.78 C \r
+ATOM 2521 CA VAL B 22 11.385 22.401 43.639 1.00 80.98 C \r
+ATOM 2528 CA TYR B 23 13.439 19.280 44.481 1.00 77.04 C \r
+ATOM 2540 CA ILE B 24 13.212 18.196 48.120 1.00 76.45 C \r
+ATOM 2548 CA LEU B 25 16.959 18.133 48.851 1.00 75.15 C \r
+ATOM 2556 CA ASP B 26 17.154 21.745 47.689 1.00 75.80 C \r
+ATOM 2564 CA GLN B 27 14.616 22.906 50.280 1.00 76.31 C \r
+ATOM 2573 CA ALA B 28 16.562 20.957 52.914 1.00 78.86 C \r
+ATOM 2578 CA GLU B 29 19.698 23.011 52.198 1.00 81.51 C \r
+ATOM 2587 CA GLU B 30 17.491 26.106 52.510 1.00 83.25 C \r
+ATOM 2596 CA ASP B 31 15.857 25.933 55.935 1.00 81.92 C \r
+ATOM 2604 CA GLY B 32 19.280 24.859 57.151 1.00 79.08 C \r
+ATOM 2608 CA ILE B 33 18.621 21.130 57.157 1.00 76.93 C \r
+ATOM 2616 CA ASP B 34 21.528 18.731 56.618 1.00 73.53 C \r
+ATOM 2624 CA LEU B 35 20.738 15.738 54.421 1.00 67.74 C \r
+ATOM 2632 CA PRO B 36 23.138 13.391 52.547 1.00 65.90 C \r
+ATOM 2639 CA TYR B 37 23.916 14.226 48.912 1.00 64.85 C \r
+ATOM 2651 CA SER B 38 26.659 13.373 46.412 1.00 62.58 C \r
+ATOM 2657 CA CYS B 39 26.193 13.603 42.652 1.00 60.99 C \r
+ATOM 2663 CA ARG B 40 22.908 15.441 43.251 1.00 58.35 C \r
+ATOM 2674 CA ALA B 41 21.699 14.108 39.886 1.00 56.38 C \r
+ATOM 2679 CA GLY B 42 19.886 10.955 40.991 1.00 56.66 C \r
+ATOM 2683 CA SER B 43 22.465 8.336 40.010 1.00 58.55 C \r
+ATOM 2689 CA CYS B 44 23.548 7.052 43.447 1.00 56.27 C \r
+ATOM 2695 CA SER B 45 22.057 5.987 46.791 1.00 58.20 C \r
+ATOM 2701 CA SER B 46 23.574 8.773 48.890 1.00 59.13 C \r
+ATOM 2707 CA CYS B 47 20.220 10.475 49.517 1.00 65.64 C \r
+ATOM 2713 CA ALA B 48 17.911 7.436 49.610 1.00 69.71 C \r
+ATOM 2718 CA GLY B 49 14.733 7.635 51.681 1.00 73.09 C \r
+ATOM 2722 CA LYS B 50 11.712 5.340 52.183 1.00 73.77 C \r
+ATOM 2731 CA VAL B 51 8.551 7.412 51.568 1.00 76.51 C \r
+ATOM 2738 CA VAL B 52 5.237 7.081 53.429 1.00 78.85 C \r
+ATOM 2745 CA SER B 53 2.180 9.376 53.647 1.00 79.57 C \r
+ATOM 2751 CA GLY B 54 2.118 10.991 50.218 1.00 76.32 C \r
+ATOM 2755 CA SER B 55 3.577 10.944 46.726 1.00 76.31 C \r
+ATOM 2761 CA VAL B 56 6.436 12.592 44.828 1.00 77.50 C \r
+ATOM 2768 CA ASP B 57 7.691 12.960 41.243 1.00 76.83 C \r
+ATOM 2776 CA GLN B 58 11.150 11.483 40.555 1.00 76.66 C \r
+ATOM 2785 CA SER B 59 10.976 10.827 36.792 1.00 80.19 C \r
+ATOM 2791 CA ASP B 60 14.688 11.644 36.510 1.00 83.51 C \r
+ATOM 2799 CA GLN B 61 15.175 8.137 37.916 1.00 85.74 C \r
+ATOM 2808 CA SER B 62 18.644 7.080 36.699 1.00 85.85 C \r
+ATOM 2814 CA TYR B 63 19.324 5.049 39.852 1.00 84.49 C \r
+ATOM 2826 CA LEU B 64 15.683 4.296 40.629 1.00 89.06 C \r
+ATOM 2834 CA ASP B 65 15.356 0.604 39.742 1.00 92.21 C \r
+ATOM 2842 CA ASP B 66 12.421 -1.791 39.331 1.00 92.35 C \r
+ATOM 2850 CA GLY B 67 10.747 -2.542 42.659 1.00 89.07 C \r
+ATOM 2854 CA GLN B 68 12.336 0.632 44.010 1.00 88.41 C \r
+ATOM 2863 CA ILE B 69 9.483 2.828 42.742 1.00 86.11 C \r
+ATOM 2871 CA ALA B 70 7.060 0.441 44.446 1.00 81.10 C \r
+ATOM 2876 CA ASP B 71 8.985 -0.310 47.648 1.00 76.82 C \r
+ATOM 2884 CA GLY B 72 8.653 3.423 48.186 1.00 73.00 C \r
+ATOM 2888 CA TRP B 73 12.342 4.386 48.095 1.00 67.93 C \r
+ATOM 2902 CA VAL B 74 13.052 8.007 47.136 1.00 63.84 C \r
+ATOM 2909 CA LEU B 75 16.093 9.940 45.892 1.00 58.37 C \r
+ATOM 2917 CA THR B 76 15.524 13.198 47.826 1.00 55.82 C \r
+ATOM 2924 CA CYS B 77 17.941 15.109 45.556 1.00 58.23 C \r
+ATOM 2930 CA HIS B 78 15.777 14.389 42.513 1.00 64.55 C \r
+ATOM 2940 CA ALA B 79 12.108 14.429 43.512 1.00 68.40 C \r
+ATOM 2945 CA TYR B 80 9.442 17.152 43.581 1.00 69.69 C \r
+ATOM 2957 CA PRO B 81 6.414 16.584 45.842 1.00 71.39 C \r
+ATOM 2964 CA THR B 82 3.015 16.014 44.179 1.00 73.67 C \r
+ATOM 2971 CA SER B 83 1.278 15.771 47.557 1.00 76.90 C \r
+ATOM 2977 CA ASP B 84 1.940 16.119 51.289 1.00 75.20 C \r
+ATOM 2985 CA VAL B 85 4.840 13.765 52.050 1.00 71.37 C \r
+ATOM 2992 CA VAL B 86 6.363 11.824 54.956 1.00 70.12 C \r
+ATOM 2999 CA ILE B 87 9.770 10.300 54.188 1.00 74.18 C \r
+ATOM 3007 CA GLU B 88 12.211 8.403 56.410 1.00 78.53 C \r
+ATOM 3012 CA THR B 89 15.541 9.964 55.407 1.00 79.79 C \r
+ATOM 3019 CA HIS B 90 19.062 8.538 55.881 1.00 79.40 C \r
+ATOM 3029 CA LYS B 91 17.584 5.099 55.099 1.00 84.52 C \r
+ATOM 3038 CA GLU B 92 20.016 2.596 53.549 1.00 91.64 C \r
+ATOM 3047 CA GLU B 93 20.192 -0.858 51.981 1.00 98.97 C \r
+ATOM 3056 CA GLU B 94 23.321 -2.924 51.298 1.00106.32 C \r
+ATOM 3065 CA LEU B 95 22.104 -6.552 51.453 1.00111.32 C \r
+ATOM 3073 CA THR B 96 18.778 -8.417 51.866 1.00116.01 C \r
+ATOM 3080 CA GLY B 97 18.877 -11.302 49.394 1.00116.63 C \r
+ATOM 3084 CA ALA B 98 22.056 -9.833 47.910 1.00116.02 C \r
+ATOM 3091 CA GLU C 19 26.080 -2.480 15.294 1.00 73.96 C \r
+ATOM 3100 CA SER C 20 23.405 0.198 14.956 1.00 67.27 C \r
+ATOM 3106 CA LYS C 21 22.937 3.927 15.380 1.00 59.27 C \r
+ATOM 3115 CA LYS C 22 19.198 3.481 15.874 1.00 58.42 C \r
+ATOM 3124 CA GLN C 23 17.251 3.141 19.137 1.00 59.89 C \r
+ATOM 3133 CA GLU C 24 17.931 -0.276 20.610 1.00 62.66 C \r
+ATOM 3142 CA GLU C 25 16.850 -0.453 24.226 1.00 64.27 C \r
+ATOM 3151 CA GLY C 26 13.211 -0.817 25.116 1.00 61.78 C \r
+ATOM 3155 CA VAL C 27 12.703 -2.073 21.582 1.00 58.37 C \r
+ATOM 3162 CA VAL C 28 10.779 -5.347 21.485 1.00 54.17 C \r
+ATOM 3169 CA THR C 29 9.481 -7.339 18.549 1.00 52.79 C \r
+ATOM 3176 CA ASN C 30 6.670 -9.775 17.786 1.00 51.30 C \r
+ATOM 3184 CA LEU C 31 4.863 -9.997 21.112 1.00 51.05 C \r
+ATOM 3192 CA TYR C 32 1.766 -11.297 19.327 1.00 50.51 C \r
+ATOM 3204 CA LYS C 33 1.373 -13.532 16.266 1.00 49.49 C \r
+ATOM 3213 CA PRO C 34 -1.609 -14.150 13.925 1.00 50.98 C \r
+ATOM 3220 CA LYS C 35 -2.450 -17.248 16.011 1.00 55.46 C \r
+ATOM 3229 CA GLU C 36 -2.977 -15.400 19.288 1.00 53.79 C \r
+ATOM 3238 CA PRO C 37 -3.251 -11.638 18.607 1.00 49.32 C \r
+ATOM 3245 CA TYR C 38 -3.674 -9.050 21.318 1.00 46.76 C \r
+ATOM 3257 CA VAL C 39 -7.276 -7.947 21.418 1.00 43.68 C \r
+ATOM 3264 CA GLY C 40 -7.415 -4.194 21.922 1.00 41.62 C \r
+ATOM 3268 CA ARG C 41 -10.273 -1.719 21.954 1.00 40.07 C \r
+ATOM 3279 CA CYS C 42 -11.026 1.064 19.477 1.00 36.37 C \r
+ATOM 3285 CA LEU C 43 -11.330 4.206 21.583 1.00 31.09 C \r
+ATOM 3293 CA LEU C 44 -11.337 6.671 18.673 1.00 28.46 C \r
+ATOM 3301 CA ASN C 45 -11.792 6.653 14.923 1.00 26.74 C \r
+ATOM 3309 CA THR C 46 -11.954 9.920 13.013 1.00 25.29 C \r
+ATOM 3316 CA LYS C 47 -11.667 10.775 9.352 1.00 21.50 C \r
+ATOM 3325 CA ILE C 48 -8.895 13.355 9.121 1.00 19.33 C \r
+ATOM 3333 CA THR C 49 -9.125 14.281 5.442 1.00 20.38 C \r
+ATOM 3340 CA GLY C 50 -11.630 16.676 3.855 1.00 20.12 C \r
+ATOM 3344 CA ASP C 51 -14.895 15.345 2.412 1.00 21.75 C \r
+ATOM 3352 CA ASP C 52 -13.889 16.693 -0.999 1.00 21.19 C \r
+ATOM 3360 CA ALA C 53 -10.651 14.683 -0.749 1.00 21.06 C \r
+ATOM 3365 CA PRO C 54 -10.036 11.974 -3.413 1.00 21.39 C \r
+ATOM 3372 CA GLY C 55 -9.982 9.067 -0.977 1.00 24.42 C \r
+ATOM 3376 CA GLU C 56 -10.374 9.298 2.857 1.00 22.08 C \r
+ATOM 3385 CA THR C 57 -7.723 8.611 5.517 1.00 20.31 C \r
+ATOM 3392 CA TRP C 58 -8.541 7.849 9.162 1.00 19.33 C \r
+ATOM 3406 CA HIS C 59 -6.758 8.520 12.438 1.00 22.68 C \r
+ATOM 3416 CA MET C 60 -7.645 5.951 15.108 1.00 27.16 C \r
+ATOM 3424 CA VAL C 61 -6.672 5.224 18.723 1.00 29.32 C \r
+ATOM 3431 CA PHE C 62 -6.669 1.704 20.220 1.00 34.23 C \r
+ATOM 3442 CA SER C 63 -6.102 0.643 23.847 1.00 37.05 C \r
+ATOM 3448 CA THR C 64 -3.096 -1.517 24.798 1.00 41.86 C \r
+ATOM 3455 CA GLU C 65 -3.169 -1.652 28.621 1.00 48.33 C \r
+ATOM 3464 CA GLY C 66 0.537 -0.885 28.318 1.00 52.45 C \r
+ATOM 3468 CA LYS C 67 0.955 -4.385 26.891 1.00 54.14 C \r
+ATOM 3477 CA ILE C 68 2.429 -3.211 23.570 1.00 51.52 C \r
+ATOM 3485 CA PRO C 69 5.602 -1.279 24.487 1.00 49.85 C \r
+ATOM 3492 CA TYR C 70 6.523 -0.180 20.967 1.00 44.48 C \r
+ATOM 3504 CA ARG C 71 9.185 2.353 19.993 1.00 40.96 C \r
+ATOM 3515 CA GLU C 72 8.727 5.317 17.688 1.00 33.49 C \r
+ATOM 3524 CA GLY C 73 8.913 3.876 14.164 1.00 30.16 C \r
+ATOM 3528 CA GLN C 74 7.423 0.399 14.427 1.00 31.26 C \r
+ATOM 3537 CA SER C 75 4.187 -0.913 12.966 1.00 33.65 C \r
+ATOM 3543 CA ILE C 76 1.454 -3.212 14.278 1.00 33.75 C \r
+ATOM 3551 CA GLY C 77 -0.295 -5.923 12.356 1.00 34.32 C \r
+ATOM 3555 CA VAL C 78 -4.060 -6.111 12.164 1.00 36.67 C \r
+ATOM 3562 CA ILE C 79 -6.137 -9.230 11.507 1.00 41.91 C \r
+ATOM 3570 CA ALA C 80 -9.427 -8.086 10.024 1.00 44.06 C \r
+ATOM 3575 CA ASP C 81 -12.530 -9.927 11.224 1.00 47.03 C \r
+ATOM 3583 CA GLY C 82 -13.972 -12.487 8.829 1.00 53.52 C \r
+ATOM 3587 CA VAL C 83 -12.521 -14.951 6.324 1.00 62.57 C \r
+ATOM 3594 CA ASP C 84 -11.856 -14.200 2.630 1.00 71.97 C \r
+ATOM 3602 CA LYS C 85 -12.935 -17.403 0.861 1.00 76.86 C \r
+ATOM 3611 CA ASN C 86 -13.690 -18.960 4.253 1.00 76.52 C \r
+ATOM 3619 CA GLY C 87 -10.006 -19.837 4.066 1.00 76.22 C \r
+ATOM 3623 CA LYS C 88 -8.802 -19.138 7.616 1.00 71.60 C \r
+ATOM 3632 CA PRO C 89 -8.651 -15.577 8.944 1.00 64.14 C \r
+ATOM 3639 CA HIS C 90 -7.547 -12.649 6.805 1.00 52.35 C \r
+ATOM 3649 CA LYS C 91 -3.753 -12.529 6.474 1.00 46.81 C \r
+ATOM 3658 CA VAL C 92 -2.180 -9.868 8.686 1.00 43.48 C \r
+ATOM 3665 CA ARG C 93 -1.491 -6.414 7.232 1.00 36.99 C \r
+ATOM 3676 CA LEU C 94 0.983 -3.882 8.601 1.00 32.95 C \r
+ATOM 3684 CA TYR C 95 0.340 -0.239 9.510 1.00 24.84 C \r
+ATOM 3696 CA SER C 96 3.003 2.101 10.803 1.00 23.32 C \r
+ATOM 3702 CA ILE C 97 2.244 3.502 14.236 1.00 24.12 C \r
+ATOM 3710 CA ALA C 98 1.243 7.179 13.932 1.00 22.32 C \r
+ATOM 3715 CA SER C 99 1.572 7.636 17.676 1.00 25.69 C \r
+ATOM 3721 CA SER C 100 4.752 7.924 19.726 1.00 28.83 C \r
+ATOM 3727 CA ALA C 101 5.741 5.521 22.508 1.00 35.61 C \r
+ATOM 3732 CA ILE C 102 3.906 7.635 25.079 1.00 38.39 C \r
+ATOM 3740 CA GLY C 103 0.899 7.826 22.742 1.00 31.93 C \r
+ATOM 3744 CA ASP C 104 -1.803 10.384 21.986 1.00 28.77 C \r
+ATOM 3752 CA PHE C 105 -3.050 10.293 25.607 1.00 37.05 C \r
+ATOM 3763 CA GLY C 106 0.503 10.389 26.967 1.00 39.36 C \r
+ATOM 3767 CA ASP C 107 -0.221 7.437 29.266 1.00 41.44 C \r
+ATOM 3775 CA SER C 108 1.566 4.766 27.217 1.00 42.18 C \r
+ATOM 3781 CA LYS C 109 -1.747 2.877 27.156 1.00 42.45 C \r
+ATOM 3790 CA THR C 110 -2.698 3.586 23.515 1.00 38.10 C \r
+ATOM 3797 CA VAL C 111 -1.603 2.971 19.906 1.00 32.79 C \r
+ATOM 3804 CA SER C 112 -2.671 5.020 16.872 1.00 29.60 C \r
+ATOM 3810 CA LEU C 113 -2.713 4.324 13.126 1.00 25.68 C \r
+ATOM 3818 CA CYS C 114 -3.142 6.498 9.999 1.00 24.23 C \r
+ATOM 3824 CA VAL C 115 -5.345 4.496 7.641 1.00 22.80 C \r
+ATOM 3831 CA LYS C 116 -6.221 5.196 4.015 1.00 22.11 C \r
+ATOM 3840 CA ARG C 117 -9.458 3.521 2.955 1.00 25.68 C \r
+ATOM 3851 CA LEU C 118 -8.447 1.440 -0.100 1.00 28.80 C \r
+ATOM 3859 CA ILE C 119 -11.140 1.661 -2.792 1.00 31.75 C \r
+ATOM 3867 CA TYR C 120 -10.086 0.716 -6.312 1.00 32.93 C \r
+ATOM 3879 CA THR C 121 -11.388 -0.733 -9.598 1.00 36.84 C \r
+ATOM 3886 CA ASN C 122 -10.258 -4.257 -10.546 1.00 36.90 C \r
+ATOM 3894 CA ASP C 123 -9.574 -5.562 -14.056 1.00 45.45 C \r
+ATOM 3902 CA ALA C 124 -13.196 -6.758 -14.269 1.00 44.66 C \r
+ATOM 3907 CA GLY C 125 -14.207 -3.102 -14.023 1.00 45.49 C \r
+ATOM 3911 CA GLU C 126 -16.059 -3.511 -10.722 1.00 45.54 C \r
+ATOM 3920 CA ILE C 127 -15.507 -1.321 -7.638 1.00 39.70 C \r
+ATOM 3928 CA VAL C 128 -13.846 -3.171 -4.762 1.00 38.09 C \r
+ATOM 3935 CA LYS C 129 -12.759 -2.512 -1.198 1.00 33.77 C \r
+ATOM 3944 CA GLY C 130 -9.566 -3.363 0.599 1.00 31.98 C \r
+ATOM 3948 CA VAL C 131 -10.443 -5.797 3.385 1.00 33.16 C \r
+ATOM 3955 CA CYS C 132 -8.241 -4.645 6.257 1.00 29.97 C \r
+ATOM 3961 CA SER C 133 -8.238 -0.898 5.607 1.00 30.67 C \r
+ATOM 3967 CA ASN C 134 -12.022 -0.902 5.268 1.00 30.35 C \r
+ATOM 3975 CA PHE C 135 -12.375 -2.946 8.424 1.00 29.86 C \r
+ATOM 3986 CA LEU C 136 -10.223 -0.334 10.195 1.00 29.42 C \r
+ATOM 3994 CA CYS C 137 -11.779 2.834 8.813 1.00 32.27 C \r
+ATOM 4000 CA ASP C 138 -15.116 1.280 9.724 1.00 34.29 C \r
+ATOM 4008 CA LEU C 139 -14.287 0.699 13.399 1.00 37.51 C \r
+ATOM 4016 CA GLN C 140 -16.635 2.170 16.028 1.00 43.76 C \r
+ATOM 4025 CA PRO C 141 -15.630 3.032 19.581 1.00 42.77 C \r
+ATOM 4032 CA GLY C 142 -16.082 -0.210 21.478 1.00 42.83 C \r
+ATOM 4036 CA ASP C 143 -15.117 -2.625 18.696 1.00 40.91 C \r
+ATOM 4044 CA ASN C 144 -12.182 -4.947 19.288 1.00 45.66 C \r
+ATOM 4052 CA VAL C 145 -9.056 -5.146 17.145 1.00 46.95 C \r
+ATOM 4059 CA GLN C 146 -6.707 -8.107 16.606 1.00 48.69 C \r
+ATOM 4068 CA ILE C 147 -3.249 -6.538 17.123 1.00 46.84 C \r
+ATOM 4076 CA THR C 148 -0.010 -8.392 16.264 1.00 46.26 C \r
+ATOM 4083 CA GLY C 149 3.543 -7.117 16.634 1.00 45.60 C \r
+ATOM 4087 CA PRO C 150 5.248 -4.818 17.394 1.00 44.97 C \r
+ATOM 4094 CA VAL C 151 7.423 -5.293 14.321 1.00 44.50 C \r
+ATOM 4101 CA GLY C 152 10.289 -3.716 12.438 1.00 45.33 C \r
+ATOM 4105 CA LYS C 153 13.599 -2.161 13.435 1.00 48.64 C \r
+ATOM 4114 CA GLU C 154 14.166 -0.437 10.074 1.00 48.20 C \r
+ATOM 4123 CA MET C 155 12.437 2.888 10.737 1.00 41.77 C \r
+ATOM 4131 CA LEU C 156 13.839 3.081 14.267 1.00 38.27 C \r
+ATOM 4139 CA MET C 157 15.076 6.540 15.308 1.00 34.29 C \r
+ATOM 4147 CA PRO C 158 18.782 7.419 15.339 1.00 34.05 C \r
+ATOM 4154 CA LYS C 159 20.262 7.521 18.845 1.00 35.82 C \r
+ATOM 4163 CA ASP C 160 22.076 10.792 18.273 1.00 35.95 C \r
+ATOM 4171 CA PRO C 161 19.683 13.401 19.809 1.00 35.63 C \r
+ATOM 4178 CA ASN C 162 21.563 15.948 17.758 1.00 33.92 C \r
+ATOM 4186 CA ALA C 163 21.028 14.172 14.487 1.00 30.82 C \r
+ATOM 4191 CA THR C 164 19.693 15.722 11.305 1.00 25.18 C \r
+ATOM 4198 CA ILE C 165 16.617 13.601 10.636 1.00 19.91 C \r
+ATOM 4206 CA ILE C 166 15.351 13.978 7.060 1.00 13.76 C \r
+ATOM 4214 CA MET C 167 11.843 12.550 6.703 1.00 14.98 C \r
+ATOM 4222 CA LEU C 168 10.385 11.831 3.251 1.00 16.64 C \r
+ATOM 4230 CA ALA C 169 6.747 10.808 3.007 1.00 15.85 C \r
+ATOM 4235 CA THR C 170 3.765 10.346 0.737 1.00 14.23 C \r
+ATOM 4242 CA GLY C 171 0.255 9.724 2.035 1.00 13.78 C \r
+ATOM 4246 CA THR C 172 -0.103 7.560 5.139 1.00 17.62 C \r
+ATOM 4253 CA GLY C 173 3.646 7.343 4.821 1.00 17.20 C \r
+ATOM 4257 CA ILE C 174 3.469 10.213 7.270 1.00 15.91 C \r
+ATOM 4265 CA ALA C 175 2.586 7.783 10.110 1.00 15.63 C \r
+ATOM 4270 CA PRO C 176 6.023 6.933 11.582 1.00 17.04 C \r
+ATOM 4277 CA PHE C 177 7.215 10.514 11.327 1.00 18.21 C \r
+ATOM 4288 CA ARG C 178 4.268 11.745 13.359 1.00 22.35 C \r
+ATOM 4299 CA SER C 179 5.563 9.289 15.983 1.00 25.22 C \r
+ATOM 4305 CA PHE C 180 9.139 10.593 15.614 1.00 25.98 C \r
+ATOM 4316 CA LEU C 181 7.925 14.180 15.767 1.00 29.12 C \r
+ATOM 4324 CA TRP C 182 5.625 13.641 18.714 1.00 31.35 C \r
+ATOM 4338 CA LYS C 183 8.488 12.385 20.871 1.00 30.92 C \r
+ATOM 4347 CA MET C 184 10.841 15.050 19.503 1.00 24.85 C \r
+ATOM 4355 CA PHE C 185 8.741 18.202 20.114 1.00 22.97 C \r
+ATOM 4366 CA PHE C 186 5.604 17.337 22.076 1.00 27.77 C \r
+ATOM 4377 CA GLU C 187 7.117 15.432 25.009 1.00 37.71 C \r
+ATOM 4386 CA LYS C 188 9.542 15.977 27.878 1.00 53.59 C \r
+ATOM 4395 CA HIS C 189 12.355 13.416 28.180 1.00 63.67 C \r
+ATOM 4405 CA ASP C 190 15.318 13.181 30.569 1.00 66.93 C \r
+ATOM 4413 CA ASP C 191 17.480 11.106 28.238 1.00 59.79 C \r
+ATOM 4421 CA TYR C 192 16.190 12.725 25.047 1.00 51.96 C \r
+ATOM 4433 CA LYS C 193 16.700 16.406 24.324 1.00 47.01 C \r
+ATOM 4442 CA PHE C 194 16.580 16.471 20.530 1.00 39.85 C \r
+ATOM 4453 CA ASN C 195 18.572 19.494 19.409 1.00 37.52 C \r
+ATOM 4461 CA GLY C 196 19.361 18.548 15.845 1.00 32.08 C \r
+ATOM 4465 CA LEU C 197 17.310 19.266 12.766 1.00 28.26 C \r
+ATOM 4473 CA GLY C 198 14.051 17.526 11.928 1.00 25.05 C \r
+ATOM 4477 CA TRP C 199 13.211 18.137 8.269 1.00 19.81 C \r
+ATOM 4491 CA LEU C 200 9.908 16.742 7.059 1.00 13.86 C \r
+ATOM 4499 CA PHE C 201 8.855 16.521 3.429 1.00 14.83 C \r
+ATOM 4510 CA LEU C 202 5.288 15.361 2.717 1.00 16.12 C \r
+ATOM 4518 CA GLY C 203 3.701 14.731 -0.681 1.00 13.79 C \r
+ATOM 4522 CA VAL C 204 -0.051 14.414 -1.182 1.00 11.75 C \r
+ATOM 4529 CA PRO C 205 -2.113 15.264 -4.308 1.00 14.66 C \r
+ATOM 4536 CA THR C 206 -4.553 17.737 -2.778 1.00 16.37 C \r
+ATOM 4543 CA SER C 207 -4.756 20.169 0.120 1.00 18.01 C \r
+ATOM 4549 CA SER C 208 -7.780 18.225 1.280 1.00 17.59 C \r
+ATOM 4555 CA SER C 209 -5.452 15.198 1.550 1.00 16.19 C \r
+ATOM 4561 CA LEU C 210 -2.972 16.940 3.860 1.00 14.22 C \r
+ATOM 4569 CA LEU C 211 -2.255 14.980 7.059 1.00 14.43 C \r
+ATOM 4577 CA TYR C 212 -1.624 16.449 10.549 1.00 18.94 C \r
+ATOM 4589 CA LYS C 213 -0.818 19.896 9.150 1.00 22.61 C \r
+ATOM 4598 CA GLU C 214 -2.039 21.572 12.352 1.00 25.73 C \r
+ATOM 4607 CA GLU C 215 0.152 19.413 14.514 1.00 19.23 C \r
+ATOM 4616 CA PHE C 216 3.216 20.178 12.439 1.00 17.80 C \r
+ATOM 4627 CA GLY C 217 2.478 23.890 12.512 1.00 19.90 C \r
+ATOM 4631 CA LYS C 218 2.578 24.001 16.294 1.00 25.54 C \r
+ATOM 4640 CA MET C 219 5.810 22.021 16.188 1.00 26.79 C \r
+ATOM 4648 CA LYS C 220 7.224 24.606 13.819 1.00 31.85 C \r
+ATOM 4657 CA GLU C 221 6.071 27.341 16.219 1.00 38.62 C \r
+ATOM 4666 CA ARG C 222 7.760 25.760 19.233 1.00 39.10 C \r
+ATOM 4677 CA ALA C 223 11.124 24.971 17.668 1.00 35.43 C \r
+ATOM 4682 CA PRO C 224 11.696 27.100 14.528 1.00 32.99 C \r
+ATOM 4689 CA GLU C 225 15.425 26.331 14.360 1.00 33.87 C \r
+ATOM 4698 CA ASN C 226 15.038 22.591 14.986 1.00 30.46 C \r
+ATOM 4706 CA PHE C 227 12.088 21.755 12.732 1.00 24.98 C \r
+ATOM 4717 CA ARG C 228 11.351 22.384 9.075 1.00 19.87 C \r
+ATOM 4728 CA VAL C 229 8.435 21.010 7.118 1.00 14.21 C \r
+ATOM 4735 CA ASP C 230 7.739 21.452 3.398 1.00 12.26 C \r
+ATOM 4743 CA TYR C 231 4.627 20.147 1.722 1.00 14.42 C \r
+ATOM 4755 CA ALA C 232 4.334 19.003 -1.872 1.00 9.99 C \r
+ATOM 4760 CA VAL C 233 0.778 19.232 -3.168 1.00 10.49 C \r
+ATOM 4767 CA SER C 234 1.043 17.769 -6.694 1.00 19.00 C \r
+ATOM 4773 CA ARG C 235 -2.240 19.042 -8.206 1.00 23.13 C \r
+ATOM 4784 CA GLU C 236 -2.069 22.459 -6.578 1.00 17.58 C \r
+ATOM 4793 CA GLN C 237 1.546 23.511 -6.623 1.00 15.89 C \r
+ATOM 4802 CA THR C 238 4.202 24.018 -9.275 1.00 17.86 C \r
+ATOM 4809 CA ASN C 239 7.922 24.800 -9.182 1.00 15.15 C \r
+ATOM 4817 CA ALA C 240 9.558 27.791 -10.892 1.00 21.51 C \r
+ATOM 4822 CA ALA C 241 9.475 25.887 -14.174 1.00 24.05 C \r
+ATOM 4827 CA GLY C 242 5.741 25.110 -13.938 1.00 26.25 C \r
+ATOM 4831 CA GLU C 243 5.999 21.359 -13.153 1.00 25.92 C \r
+ATOM 4840 CA ARG C 244 3.679 19.536 -10.704 1.00 24.04 C \r
+ATOM 4851 CA MET C 245 5.076 19.643 -7.174 1.00 18.58 C \r
+ATOM 4859 CA TYR C 246 5.784 16.047 -6.100 1.00 14.16 C \r
+ATOM 4871 CA ILE C 247 7.910 15.343 -3.034 1.00 16.78 C \r
+ATOM 4879 CA GLN C 248 11.089 15.070 -5.120 1.00 18.72 C \r
+ATOM 4888 CA THR C 249 10.168 18.255 -6.921 1.00 20.93 C \r
+ATOM 4895 CA ARG C 250 9.962 20.031 -3.567 1.00 19.25 C \r
+ATOM 4906 CA MET C 251 13.275 18.471 -2.561 1.00 19.40 C \r
+ATOM 4914 CA ALA C 252 14.910 19.812 -5.760 1.00 20.48 C \r
+ATOM 4919 CA GLU C 253 14.456 23.418 -4.569 1.00 18.19 C \r
+ATOM 4928 CA TYR C 254 16.804 22.515 -1.673 1.00 17.80 C \r
+ATOM 4940 CA LYS C 255 19.038 20.415 -3.902 1.00 20.66 C \r
+ATOM 4949 CA GLU C 256 22.452 21.603 -2.682 1.00 16.05 C \r
+ATOM 4958 CA GLU C 257 21.544 21.914 0.993 1.00 15.89 C \r
+ATOM 4967 CA LEU C 258 20.377 18.297 0.919 1.00 20.74 C \r
+ATOM 4975 CA TRP C 259 23.388 16.939 -0.965 1.00 23.45 C \r
+ATOM 4989 CA GLU C 260 25.645 18.669 1.563 1.00 24.08 C \r
+ATOM 4998 CA LEU C 261 23.573 17.378 4.477 1.00 24.74 C \r
+ATOM 5006 CA LEU C 262 24.020 13.928 2.938 1.00 26.14 C \r
+ATOM 5014 CA LYS C 263 27.792 14.091 3.402 1.00 25.40 C \r
+ATOM 5023 CA LYS C 264 27.457 14.521 7.176 1.00 31.47 C \r
+ATOM 5032 CA ASP C 265 27.877 11.474 9.425 1.00 35.31 C \r
+ATOM 5040 CA ASN C 266 24.934 12.482 11.620 1.00 29.63 C \r
+ATOM 5048 CA THR C 267 22.321 12.795 8.832 1.00 28.00 C \r
+ATOM 5055 CA TYR C 268 19.556 10.160 8.808 1.00 27.00 C \r
+ATOM 5067 CA VAL C 269 17.143 9.903 5.884 1.00 24.65 C \r
+ATOM 5074 CA TYR C 270 13.890 8.016 6.276 1.00 23.37 C \r
+ATOM 5086 CA MET C 271 11.373 7.327 3.518 1.00 18.93 C \r
+ATOM 5094 CA CYS C 272 7.834 6.074 4.043 1.00 18.24 C \r
+ATOM 5100 CA GLY C 273 4.784 5.874 1.826 1.00 22.39 C \r
+ATOM 5104 CA LEU C 274 3.837 4.483 -1.568 1.00 26.95 C \r
+ATOM 5112 CA LYS C 275 6.305 2.384 -3.532 1.00 32.36 C \r
+ATOM 5121 CA GLY C 276 7.741 4.199 -6.514 1.00 37.46 C \r
+ATOM 5125 CA MET C 277 7.714 7.455 -4.608 1.00 28.76 C \r
+ATOM 5133 CA GLU C 278 11.430 6.639 -4.425 1.00 32.22 C \r
+ATOM 5142 CA LYS C 279 12.017 6.321 -8.153 1.00 29.94 C \r
+ATOM 5151 CA GLY C 280 11.317 10.057 -8.293 1.00 24.18 C \r
+ATOM 5155 CA ILE C 281 13.766 10.673 -5.460 1.00 23.68 C \r
+ATOM 5163 CA ASP C 282 16.431 8.365 -6.934 1.00 26.58 C \r
+ATOM 5171 CA ASP C 283 16.211 10.530 -10.054 1.00 28.70 C \r
+ATOM 5179 CA ILE C 284 17.089 13.937 -8.538 1.00 27.28 C \r
+ATOM 5187 CA MET C 285 19.706 12.222 -6.388 1.00 27.45 C \r
+ATOM 5195 CA VAL C 286 21.377 10.712 -9.470 1.00 30.74 C \r
+ATOM 5202 CA SER C 287 21.619 14.159 -11.061 1.00 32.14 C \r
+ATOM 5208 CA LEU C 288 23.240 15.463 -7.873 1.00 34.20 C \r
+ATOM 5216 CA ALA C 289 25.801 12.653 -7.874 1.00 40.16 C \r
+ATOM 5221 CA GLU C 290 26.837 12.825 -11.536 1.00 41.84 C \r
+ATOM 5230 CA LYS C 291 27.855 16.387 -10.793 1.00 43.17 C \r
+ATOM 5239 CA ASP C 292 30.299 15.115 -8.139 1.00 41.84 C \r
+ATOM 5247 CA GLY C 293 31.237 12.232 -10.420 1.00 46.12 C \r
+ATOM 5251 CA ILE C 294 30.053 9.669 -7.864 1.00 45.54 C \r
+ATOM 5259 CA ASP C 295 27.399 6.998 -8.480 1.00 41.14 C \r
+ATOM 5267 CA TRP C 296 24.222 7.605 -6.479 1.00 30.67 C \r
+ATOM 5281 CA PHE C 297 23.381 3.910 -6.151 1.00 31.97 C \r
+ATOM 5292 CA ASP C 298 26.856 2.916 -4.907 1.00 38.12 C \r
+ATOM 5300 CA TYR C 299 26.671 5.875 -2.540 1.00 39.05 C \r
+ATOM 5312 CA LYS C 300 23.196 4.971 -1.294 1.00 41.63 C \r
+ATOM 5321 CA LYS C 301 24.542 1.489 -0.577 1.00 43.40 C \r
+ATOM 5330 CA GLN C 302 27.207 3.064 1.608 1.00 43.79 C \r
+ATOM 5339 CA LEU C 303 24.476 5.181 3.238 1.00 41.51 C \r
+ATOM 5347 CA LYS C 304 22.138 2.343 4.264 1.00 45.18 C \r
+ATOM 5356 CA ARG C 305 25.322 0.535 5.256 1.00 46.65 C \r
+ATOM 5367 CA GLY C 306 25.613 3.181 7.945 1.00 40.29 C \r
+ATOM 5371 CA ASP C 307 21.954 3.487 8.940 1.00 41.21 C \r
+ATOM 5379 CA GLN C 308 21.463 6.730 7.023 1.00 35.55 C \r
+ATOM 5388 CA TRP C 309 18.961 5.674 4.361 1.00 31.22 C \r
+ATOM 5402 CA ASN C 310 16.018 3.728 5.752 1.00 31.61 C \r
+ATOM 5410 CA VAL C 311 13.120 2.841 3.452 1.00 32.13 C \r
+ATOM 5417 CA GLU C 312 9.705 1.332 4.261 1.00 31.51 C \r
+ATOM 5426 CA VAL C 313 7.466 1.606 1.209 1.00 26.39 C \r
+ATOM 5433 CA TYR C 314 4.403 -0.343 0.111 1.00 25.42 C \r
--- /dev/null
+# STOCKHOLM 1.0
+#=GF ID Fer2
+#=GF AC PF00111.22
+#=GF DE 2Fe-2S iron-sulfur cluster binding domain
+#=GF PI fer2;
+#=GF AU Sonnhammer ELL
+#=GF SE Prosite
+#=GF GA 20.70 15.00;
+#=GF TC 20.70 15.70;
+#=GF NC 20.60 14.90;
+#=GF BM hmmbuild HMM.ann SEED.ann
+#=GF SM hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
+#=GF TP Domain
+#=GF WK Ferredoxin
+#=GF DR INTERPRO; IPR001041;
+#=GF DR PROSITE; PDOC00175;
+#=GF DR PROSITE; PDOC00642;
+#=GF DR SCOP; 3fxc; fa;
+#=GF DR HOMSTRAD; fer2;
+#=GF DR HOMSTRAD; Ald_Xan_dh_1;
+#=GF SQ 206
+#=GS FER_GLEJA/8-82 AC P00233.1
+#=GS FER2_RAPSA/9-84 AC P14937.1
+#=GS Q39648_CITSI/61-136 AC Q39648.1
+#=GS FER3_MAIZE/63-138 AC P27788.1
+#=GS FER6_MAIZE/66-141 AC P94044.1
+#=GS FER1_SYNP2/9-83 AC P31965.2
+#=GS FER1_EQUAR/7-81 AC P00235.1
+#=GS FER2_EQUAR/7-80 AC P00237.1
+#=GS FER2_EQUAR/7-80 DR PDB; 1WRI A; 7-80;
+#=GS FER2_PLEBO/10-85 AC P46035.2
+#=GS P95533_PSEPU/253-328 AC P95533.1
+#=GS KSHB_MYCTU/273-348 AC P96853.1
+#=GS Q44253_ACISP/251-326 AC Q44253.1
+#=GS Q59656_PLEBO/573-647 AC Q59656.1
+#=GS P71846_MYCTU/600-675 AC P71846.3
+#=GS O84985_PSEPU/271-347 AC O84985.2
+#=GS PAAE_ECOLI/266-342 AC P76081.1
+#=GS HCR_ECOLI/241-316 AC P75824.3
+#=GS O87803_PSEST/5-82 AC O87803.2
+#=GS TMOF_PSEME/4-81 AC Q03304.1
+#=GS O32476_PSESP/4-81 AC O32476.1
+#=GS Q51944_BURPI/5-82 AC Q51944.1
+#=GS Q53028_RHOCO/4-80 AC Q53028.1
+#=GS Q45344_BURPI/10-88 AC Q45344.1
+#=GS Q9ZNP1_COMTE/9-88 AC Q9ZNP1.1
+#=GS Q9Z418_PSEPU/11-90 AC Q9Z418.1
+#=GS Q9ZAN6_9BURK/12-91 AC Q9ZAN6.1
+#=GS FERN_PSEPU/7-85 AC P23263.1
+#=GS O24827_ACISP/7-85 AC O24827.1
+#=GS FERX_PSEPU/8-86 AC P23103.1
+#=GS Q52061_PSEPU/8-86 AC Q52061.1
+#=GS Q52167_PSEPU/8-86 AC Q52167.1
+#=GS O84964_9RALS/4-82 AC O84964.1
+#=GS Q9Z3W9_9SPHN/8-85 AC Q9Z3W9.1
+#=GS DMPP_PSEUF/5-82 AC P19734.3
+#=GS O84963_9RALS/4-81 AC O84963.1
+#=GS Q52574_PSESP/5-83 AC Q52574.1
+#=GS Q9ZNP2_COMTE/5-82 AC Q9ZNP2.1
+#=GS Q43983_ACICA/5-82 AC Q43983.1
+#=GS O87617_PSEAE/3-78 AC O87617.1
+#=GS O52378_9RALS/3-78 AC O52378.1
+#=GS Q51492_PSEAE/3-78 AC Q51492.1
+#=GS NDOR_PSEPU/3-78 AC Q52126.1
+#=GS Q52140_PSEPU/3-78 AC Q52140.1
+#=GS Q9Z9X8_9GAMM/242-317 AC Q9Z9X8.1
+#=GS VANB_PSEUH/234-309 AC O05617.1
+#=GS VANB_PSES9/231-306 AC P12580.1
+#=GS VANB_PSEPU/231-307 AC O54037.1
+#=GS VANB_ACIAD/234-309 AC O24840.1
+#=GS O88034_STRCO/230-305 AC O88034.1
+#=GS P94680_COMTE/234-309 AC P94680.1
+#=GS CBAB_COMTE/232-307 AC Q44257.2
+#=GS POBB_PSEPS/236-311 AC Q52186.1
+#=GS YEAX_ECOLI/237-313 AC P76254.1
+#=GS Q47914_SPHCR/241-316 AC Q47914.2
+#=GS PDR_BURCE/241-314 AC P33164.3
+#=GS PDR_BURCE/241-314 DR PDB; 2PIA A; 240-313;
+#=GS PHT2_PSEPU/243-316 AC Q05182.1
+#=GS O86347_MYCTU/231-301 AC O86347.3
+#=GS YFAE_ECOLI/4-77 AC P0ABW3.1
+#=GS Y1309_HAEIN/3-75 AC P45154.1
+#=GS O31003_VIBAN/5-73 AC O31003.1
+#=GS RFBI_SALTY/5-76 AC P26395.1
+#=GS P95461_9PSED/17-94 AC P95461.1
+#=GS O85971_SPHAR/13-90 AC O85971.1
+#=GS XYLA_PSEPU/20-97 AC P21394.1
+#=GS YCBX_ECOLI/293-362 AC P75863.1
+#=GS P96096_THIFE/9-86 AC P96096.1
+#=GS MMOC_METTR/7-81 AC Q53563.1
+#=GS O85675_ACIAD/8-85 AC O85675.1
+#=GS BENC_ACIAD/19-98 AC P07771.2
+#=GS BENC_ACIAD/19-98 DR PDB; 1KRH B; 9-88;
+#=GS BENC_ACIAD/19-98 DR PDB; 1KRH A; 9-88;
+#=GS XYLZ_PSEPU/8-86 AC P23101.1
+#=GS CBDC_BURCE/8-85 AC Q51603.1
+#=GS O66892_AQUAE/7-72 AC O66892.1
+#=GS O85226_PSEFL/27-86 AC O85226.1
+#=GS O29575_ARCFU/14-75 AC O29575.1
+#=GS O27878_METTH/21-82 AC O27878.1
+#=GS Y092_METJA/14-73 AC Q57557.1
+#=GS FER5_RHOCA/10-107 AC P37097.2
+#=GS Q44501_AZOVI/10-107 AC Q44501.1
+#=GS Q46508_DESFR/6-74 AC Q46508.1
+#=GS Q9ZBV9_STRCO/15-78 AC Q9ZBV9.1
+#=GS NUOG_MYCTU/19-82 AC P95175.2
+#=GS O87815_CUPNE/22-85 AC O87815.1
+#=GS NQO3_THET8/4-88 AC Q56223.2
+#=GS NQO3_THET8/4-88 DR PDB; 3M9S C; 4-88;
+#=GS NQO3_THET8/4-88 DR PDB; 3M9S 3; 4-88;
+#=GS P74022_SYNY3/6-69 AC P74022.1
+#=GS P94157_SYNP6/6-69 AC P94157.1
+#=GS Q44513_ANAVA/6-69 AC Q44513.1
+#=GS P77908_MOOTH/4-67 AC P77908.3
+#=GS Q9ZJW1_HELPJ/4-65 AC Q9ZJW1.1
+#=GS O05397_BACSU/11-72 AC O05397.1
+#=GS YJGC_BACSU/7-68 AC O34720.1
+#=GS NUOG_SALTI/4-72 AC P0A1Y5.2
+#=GS O66748_AQUAE/6-70 AC O66748.1
+#=GS NDUS1_DICDI/5-71 AC Q34312.1
+#=GS NQO3_PARDE/7-71 AC P29915.4
+#=GS NDUS1_NEUCR/38-101 AC P24918.2
+#=GS NUOG_RICPR/4-67 AC Q9ZCF6.1
+#=GS NDUS1_SOLTU/70-133 AC Q43644.1
+#=GS NDUS1_RECAM/4-67 AC O21241.1
+#=GS NDUS1_BOVIN/34-97 AC P15690.1
+#=GS O52683_THEMA/3-65 AC O52683.1
+#=GS Q46606_DESVU/3-71 AC Q46606.1
+#=GS HOXU_CUPNH/5-66 AC P22318.2
+#=GS P72305_RHOOP/5-66 AC P72305.1
+#=GS Q59261_CLOSA/4-67 AC Q59261.1
+#=GS Q9ZNE4_CLOPE/4-67 AC Q9ZNE4.1
+#=GS PHF1_CLOPA/4-67 AC P29166.1
+#=GS Q59262_CLOAB/4-66 AC Q59262.1
+#=GS P74801_SYNY3/5-63 AC P74801.1
+#=GS XDHE_BACSU/18-77 AC O32143.1
+#=GS HCRC_THAAR/7-66 AC O33818.1
+#=GS HCRC_THAAR/7-66 DR PDB; 1SB3 F; 7-66;
+#=GS HCRC_THAAR/7-66 DR PDB; 1RM6 C; 7-66;
+#=GS HCRC_THAAR/7-66 DR PDB; 1RM6 F; 7-66;
+#=GS HCRC_THAAR/7-66 DR PDB; 1SB3 C; 7-66;
+#=GS P95635_RHOPA/15-74 AC P95635.1
+#=GS XDHC_ECOLI/11-69 AC Q46801.1
+#=GS YAGT_ECOLI/65-124 AC P77165.1
+#=GS DCMS_HYDPS/8-67 AC P19915.2
+#=GS Q52589_9PSED/8-67 AC Q52589.1
+#=GS O52837_BRAJA/6-65 AC O52837.1
+#=GS O53709_MYCTU/5-64 AC O53709.1
+#=GS O87682_ARTNI/8-67 AC O87682.1
+#=GS Q59128_ARTNI/14-73 AC Q59128.1
+#=GS P72223_PSEPU/14-73 AC P72223.1
+#=GS P72223_PSEPU/14-73 DR PDB; 1T3Q A; 14-73;
+#=GS P72223_PSEPU/14-73 DR PDB; 1T3Q D; 14-73;
+#=GS Q9ZBN8_STRCO/5-65 AC Q9ZBN8.1
+#=GS O54050_RHOCA/5-68 AC O54050.1
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO A; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 E; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3R C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W54 C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W55 G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 2W3S C; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRO G; 5-68;
+#=GS O54050_RHOCA/5-68 DR PDB; 1JRP C; 5-68;
+#=GS O23887_MAIZE/15-85 AC O23887.1
+#=GS ALDO4_ARATH/8-78 AC Q7G191.2
+#=GS ALDO1_ARATH/23-95 AC Q7G193.2
+#=GS O30328_ACEEU/4-63 AC O30328.1
+#=GS IORA_BREDI/4-64 AC Q51697.1
+#=GS XDH_EMENI/39-108 AC Q12553.2
+#=GS O61198_CAEEL/8-78 AC O61198.2
+#=GS O17892_CAEEL/18-86 AC O17892.1
+#=GS XDH_DROSU/13-83 AC P91711.1
+#=GS O17506_BOMMO/19-89 AC O17506.1
+#=GS Q17250_BOMMO/18-88 AC Q17250.2
+#=GS ADO_BOVIN/9-79 AC P48034.2
+#=GS XDH_BOVIN/8-78 AC P80457.4
+#=GS XDH_BOVIN/8-78 DR PDB; 1V97 B; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVY A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVY J; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NRZ J; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVV A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NRZ A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1N5X A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1N5X B; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1V97 A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1VDV A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NVV J; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 1VDV B; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NS1 A; 8-78;
+#=GS XDH_BOVIN/8-78 DR PDB; 3NS1 J; 8-78;
+#=GS MOP_DESGI/6-65 AC Q46509.1
+#=GS MOP_DESGI/6-65 DR PDB; 1VLB A; 6-65;
+#=GS MOP_DESGI/6-65 DR PDB; 1SIJ A; 6-65;
+#=GS O53669_MYCTU/13-78 AC O53669.1
+#=GS O29566_ARCFU/5-80 AC O29566.1
+#=GS O30225_ARCFU/5-84 AC O30225.1
+#=GS NQRF_CHLTR/46-122 AC O84745.1
+#=GS NQRF_HAEIN/43-119 AC O05012.1
+#=GS NQRF_VIBAL/39-115 AC Q56584.1
+#=GS O84062_CHLTR/8-83 AC O84062.1
+#=GS Q9Z8H9_CHLPN/8-83 AC Q9Z8H9.1
+#=GS CSMJ_CHLTE/5-82 AC O68983.1
+#=GS CSMI_CHLTE/5-82 AC O68988.1
+#=GS FER_TRIVA/13-90 AC P21149.1
+#=GS FER_TRIVA/13-90 DR PDB; 1L5P A; 5-83;
+#=GS FER_TRIVA/13-90 DR PDB; 1L5P C; 5-83;
+#=GS FER_TRIVA/13-90 DR PDB; 1L5P B; 5-83;
+#=GS P73774_SYNY3/7-88 AC P73774.1
+#=GS FER_BUCAP/10-92 AC O51882.1
+#=GS O69222_AZOVI/11-93 AC O69222.1
+#=GS FER_HAEIN/10-92 AC P44428.2
+#=GS FER_PSEAE/10-92 AC Q51383.2
+#=GS ADRX_YEAST/67-149 AC Q12184.1
+#=GS ADX_PIG/71-155 AC P00258.2
+#=GS FER2_RICPR/11-93 AC Q9ZDW6.1
+#=GS O49551_ARATH/44-127 AC O49551.1
+#=GS ETP1_SCHPO/525-592 AC Q10361.2
+#=GS ETP1_SCHPO/525-592 DR PDB; 2WLB A; 525-607;
+#=GS ETP1_SCHPO/525-592 DR PDB; 2WLB B; 525-607;
+#=GS O07876_SPHSX/8-91 AC O07876.1
+#=GS Q9ZAM5_SPHSX/8-91 AC Q9ZAM5.1
+#=GS FER2_CAUCR/8-91 AC P37098.1
+#=GS FER6_RHOCA/7-91 AC P80306.1
+#=GS FER6_RHOCA/7-91 DR PDB; 1UWM A; 7-91;
+#=GS P74447_SYNY3/31-113 AC P74447.1
+#=GS P73171_SYNY3/7-85 AC P73171.1
+#=GS FER1_AQUAE/3-83 AC O67065.1
+#=GS FER4_RHOCA/7-86 AC P16022.1
+#=GS P74283_SYNY3/5-88 AC P74283.1
+#=GS PUTX_PSEPU/8-92 AC P00259.3
+#=GS PUTX_PSEPU/8-92 DR PDB; 1PDX A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR C; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP C; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQR A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1YJJ A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S C; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQQ B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLP B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1R7S B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1OQQ A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLN B; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1YJI A; 7-91;
+#=GS PUTX_PSEPU/8-92 DR PDB; 1XLN A; 7-91;
+#=GS TERPB_PSESP/8-92 AC P33007.2
+#=GS P95277_MYCTU/9-84 AC P95277.1
+#=GS O05933_PSEPU/11-88 AC O05933.1
+#=GS DESET_MYCTU/303-373 AC O05875.1
+#=GS O23344_ARATH/57-131 AC O23344.1
+#=GS P74159_SYNY3/11-86 AC P74159.1
+#=GS FER2_SYNP6/8-83 AC P08451.2
+#=GS P73388_SYNY3/9-84 AC P73388.1
+#=GS FER1_HALMA/35-108 AC P00217.2
+#=GS P74449_SYNY3/11-88 AC P74449.1
+#=GS FER2_NOSMU/10-85 AC P00249.2
+#=GS FER2_APHSA/10-86 AC P00251.2
+#=GS FER1_CYAPA/10-85 AC P17007.3
+#=GS FER_PORPU/10-85 AC P51320.2
+#=GS FER_ODOSI/10-85 AC P49522.2
+#=GS FER_BUMFI/9-84 AC P13106.1
+#=GS FER3_CYACA/9-84 AC P00241.1
+#=GS FER2_CYACA/8-83 AC P15789.1
+#=GS FER_BRYMA/8-83 AC P07838.1
+#=GS FER_APHSA/9-83 AC P00250.2
+#=GS FER_THEVL/9-84 AC P0A3D1.2
+#=GS FER_PERBI/6-80 AC P10770.1
+#=GS FER3_RAPSA/8-82 AC P14938.1
+#=GS FER1_SPIOL/58-132 AC P00221.2
+#=GS FER_SILPR/57-131 AC P04669.1
+#=GS FER_WHEAT/54-128 AC P00228.2
+#=GS FER_SAMNI/8-82 AC P00226.1
+#=GS FERA_ALOMA/8-82 AC P81372.1
+#=GS FER_ARCLA/8-82 AC P00223.1
+#=GS FER_DATST/8-82 AC P68165.1
+#=GS FER_PALPL/9-83 AC P07484.1
+#=GS FER_EUGVI/8-82 AC P22341.1
+#=GS FER_CHLFU/6-80 AC P56408.1
+#=GS FER_SYNY4/9-83 AC P00243.2
+#=GS FER1_PHYAM/8-82 AC P00229.1
+#=GS FER2_PHYAM/9-83 AC P00231.1
+#=GS FER2_SPIOL/8-82 AC P00224.1
+#=GS FER_PHYPA/57-132 AC O04166.1
+#=GS FER_MARPO/7-81 AC P09735.1
+FER_GLEJA/8-82 LTPDGE...RTIEVPDDKF.ILDAGE...E.A.GLDLPYSCRA.......GA....CSSCTGKLLDGRV.....DQSE...QSFLDDDQMAEGFV.....................LTCVAYPA
+FER2_RAPSA/9-84 IGPEGE..ENEFEVQDDQF.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGQIVKGQV.....DQSE...GSFLEDDHFEKGFV.....................LTCVAYPQ
+Q39648_CITSI/61-136 IGPMGE..EHEFEAQEDQY.ILDAAE...E.A.GVDLPYSCRA.......GA....CSTCAGKLVSGSV.....DQSD...GSFLDDNQMEAGYL.....................LTCISYPT
+FER3_MAIZE/63-138 VGPEGE..EHEFDAPDDAY.ILDAAE...T.A.GVELPYSCRA.......GA....CSTCAGKIESGSV.....DQSD...GSFLDDGQQEEGYV.....................LTCVSYPK
+FER6_MAIZE/66-141 VGPDGT..EHEFEAPDDTY.ILEAAE...T.A.GVELPFSCRA.......GS....CSTCAGRMSAGEV.....DQSE...GSFLDDGQMAEGYL.....................LTCISYPK
+FER1_SYNP2/9-83 ITPDGE...VSYDAPDDEY.ILDSAG...D.A.GYDLPASCRA.......GA....CSTCAGKIVSGTV.....DQSE...QSFLDDDQIEAGYV.....................LTCIAYPQ
+FER1_EQUAR/7-81 KTPSGE...FTLDVPEGTT.ILDAAE...E.A.GYDLPFSCRA.......GA....CSSCLGKVVSGSV.....DESE...GSFLDDGQMEEGFV.....................LTCIAIPE
+FER2_EQUAR/7-80 KTPDGD...ITFDVEPGER.LIDIGS...E.K..ADLPLSCQA.......GA....CSTCLGKIVSGTV.....DQSE...GSFLDDEQIEQGYV.....................LTCIAIPE
+#=GR FER2_EQUAR/7-80 SS E-----...EEEEE-----.TT----...-.S..S----SS--.......--....-STT---EEE-EE.....E---...-----HHHHH----.....................-TTT-EEE
+FER2_PLEBO/10-85 NKKRNL..DITLPVDEDTT.VLEAAE...E.A.ELDLPFSCHS.......GA....CSSCVGKVVEGEI.....NQDD...QTFLDEEQVAKGFV.....................LLCVTYPR
+P95533_PSEPU/253-328 VLMKGQ..THAVPVRAGEL.LLSAML...R.A.GLPAPHACRV.......GE....CASCMCRLQAGEVQ....RLDS....SVLDEDDVAAG.W...................L.LACRTRAA
+KSHB_MYCTU/273-348 VELDGQ..THTVSWPRTAK.LLDVLL...A.A.GLDAPFSCRE.......GH....CGACACTLRAGKVN....MGVN....DVLEQQDLDEG.L...................I.LACQSRPE
+Q44253_ACISP/251-326 FMLNGI..KNSVMCSEDDFILNEIIK......AGINVPSSCCA.......GN....CGSCMCLLVSGDVI....LESN....TVLDASDEEDGWI.....................LACRSKPR
+Q59656_PLEBO/573-647 FAQSGK....EITCTQDDL.ILDIAD.....QAEVAIESSCRS.......GT....CGSCKCTLLEGEV.....SYDS..EPDVLDEHDRASGQI.....................LTCIARPV
+P71846_MYCTU/600-675 FTLSGQ..RAIFDLVPGDS.ILEGAL...G..LRSDAPYACMG.......GA....CGTCRAKLIEGNVE....MD....HNFALRKAELDAGYI.....................LTCQSHPT
+O84985_PSEPU/271-347 VISDGR..ALTFDLPRNTQNVLDAGN...A.I.GAELPYSCKA.......GV....CSTCKCRVIEGEV.....EMDS...NHALEDYEVAAGYV.....................LSCQTYPV
+PAAE_ECOLI/266-342 VRQDGR..DREIVLNADDESILDAAL...R.Q.GADLPYACKG.......GV....CATCKCKVLRGKV.....AMET...NYSLEPDELAAGYV.....................LSCQALPL
+HCR_ECOLI/241-316 FTKLQP..AREFYAPVGTT.LLEALE.....SNNVPVVAACRA.......GV....CGCCKTKVVSGEY.....TVSS...TMTLTDAEIAEGYV.....................LACSCHPQ
+O87803_PSEST/5-82 IKIADT..DVEFTISDRDT.ILRAAL...R.D.GIPISYECNS.......GG....CGSCKIDVVEGQVE...TLWGE...APGLSPRDKRK.SR...................K.LACQCLAS
+TMOF_PSEME/4-81 IQSDDL..LHHFEADSNDT.LLSAAL...R.A.ELVFPYECNS.......GG....CGACKIELLEGEVS...NLWPD...APGLAARELRK.NR...................F.LACQCKPL
+O32476_PSESP/4-81 LKIEGQ..APGTCG.SGKS.LLVSAL...A.N.GIGFPYECAS.......GG....CGVCKFELLEGNVQ...SMWPD...APGLSSRDREKGNR...................H.LACQCVAL
+Q51944_BURPI/5-82 ITIEGG..SAFSVAADEDT.LLRGAL...R.G.GIALPHECSV.......GG....CGACRFDLLSGLVE...SIWPE...APGLSERDRKR.GK...................H.LACQSRPL
+Q53028_RHOCO/4-80 INVQPF..SHEYSCEDGES.LLDGAL..RN...SLLLKYGCKH.......GG....CGTCKVRLLDGDV.....EEPG..SSFALTPEDRENDVI.....................LACASVPL
+Q45344_BURPI/10-88 YAWNRP..RSTTHARPPKA.SLTGML...R.LGRKGIPVGCVN.......GG....CGVCKVRVLDGST......RLGR.RQPCPRQRRRRSAGL...................T.LACREAPL
+Q9ZNP1_COMTE/9-88 VSVEQT..GDTYACGTHES.LLSGML...R.LGRKGIPVGCVN.......GG....CGVCKVQVLEGAV.....RHLGP.VSCAHVSDLERDQGY...................T.LACRVAPL
+Q9Z418_PSEPU/11-90 VHVMQT..GETFPCATDES.LLQGML...R.LGRKGIPVGCVN.......GG....CGVCKVHVIEGQC.....RPLGP.VSRAHVSAAEEARGF...................T.LACRVAPV
+Q9ZAN6_9BURK/12-91 VHVAQT..DETFPCAGNES.LLTGMV...R.LGRKGIPVGCVN.......GG....CGVCKVRIVEGQI.....KALGP.ISRAHVTLDEENQGY...................T.LACRVAPQ
+FERN_PSEPU/7-85 ITVQPG..GERFVCQPQQS.ALHAME...T.QGKRCLPVGCRG.......GG....CGLCKVRVLAGDY......ESGR.VSCKHLPVEAREQGY...................A.LACRLFAR
+O24827_ACISP/7-85 ITEQCS..GQRFPCKAGQS.VLKAME...Q.QGLECAPVGCRG.......GG....CGLCKVTVREGDY......ECGK.MSRVHAPPEALAQGE...................V.LACRIYPL
+FERX_PSEPU/8-86 VFEVLS..GQSFRCAEGQS.VLRAME...A.QGKRCIPVGCRG.......GG....CGLCRVRVLSGAY......RSGR.MSRGHVPAKAAAEAL...................A.LACQVFPQ
+Q52061_PSEPU/8-86 IRETVS..GQTFRCLPDQS.VLSAME...Q.QGKRCVPVGCRG.......GG....CGLCKVRVLSGTY......QCHK.MSCNHVPPEAAKQGL...................A.LACQLFPQ
+Q52167_PSEPU/8-86 VHETNS..GQSFTCRPDQS.VLRAME...E.QGKRCVPVGCRG.......GG....CGLCKVRVLSGDY......QCGR.MSCSQVPPEAAQQGL...................A.LACQLYPR
+O84964_9RALS/4-82 VEIADS..GQRYPCDPGQN.LLRAME...V.LGQRGIPAGCRG.......GG....CGVCKVRIESGRY......RTGK.MSRACLSEAEQGQGL...................V.LACKAFPD
+Q9Z3W9_9SPHN/8-85 IRILGG..GQ.FACPEGER.VLIAME...Q.FGSSDIGVGCRG.......GG....CGFCLVRVVEGEY......RTGK.MSTAKVSVADQAKGY...................A.LACRIYPM
+DMPP_PSEUF/5-82 VTIEPT..GEVIEVEDGQT.ILQAAL...R.Q.GVWLPFACGH.......GT....CATCKVQVVEGEVD...IGEAS...PFALMDIERDERKV.....................LACCAIPL
+O84963_9RALS/4-81 LTIEPI..GQTIPIAPGQT.VLDACL...R.S.GVWLPHACCH.......GL....CATCKVQVVEGEVD...QGEAS..SFALMDFER.DNGQC.....................LACCATAQ
+Q52574_PSESP/5-83 LTIEPL..GRTLDVAEGQT.LLDAAL...R.S.GVYIPHACGH.......GL....CGTCKVQVTSGEVD...HGAAN..PLRRSWISSGEEGKT.....................LACCATAL
+Q9ZNP2_COMTE/5-82 LTLEPL..GASIEVEEGQT.LLDAAL...R.Q.GIYIPHACGH.......GL....CGTCKIQVCDGDVD...HGAAN..PFALMDMER.EDGMT.....................LACCATLQ
+Q43983_ACICA/5-82 VTIEPA..GTIIQVEEDQT.ILDAAL...R.Q.GVWLPFACGH.......GT....CGTCKVQVTDGFYD...VGEAS..PFALMDIER.EENKV.....................LACCCKPE
+O87617_PSEAE/3-78 LHIQPL..GQTLSVDSGAN.LLEALR...A.AE.VPISYSCMA.......GR....CGTCRCKVLKGQV......L..E.SGREATLTNPHADDY...................V.LACMSAIT
+O52378_9RALS/3-78 LVVEPL..NLHLNAETGST.LLDVLR...S.NE.VPISYSCMS.......GR....CGTCRCRVIAGHL......R..D.NGPETGRPQAGKGTY...................V.LACQAVLT
+Q51492_PSEAE/3-78 LLVLPN..NRRLPFDSGAN.LLEVLR...E.HR.VGISYSCMS.......GR....CGTCRCRVIDGSV......I..S.SAAKSGDSNRIEEHY...................V.LACQSVLT
+NDOR_PSEPU/3-78 LLIQPN..NRIIPFSAGAN.LLEVLR...E.NG.VAISYSCLS.......GR....CGTCRCRVIDGSV......I..D.SGAENGQSNLTDKQY...................V.LACQSVLT
+Q52140_PSEPU/3-78 LLIQPN..NRLISFSPGAN.LLEVLR...E.NG.VAISYSCMS.......GR....CGTCRCRVTDGSV......I..D.SGTGSGLPHLVDEHY...................V.LACRSVLT
+Q9Z9X8_9GAMM/242-317 VRIASS..GATVHVDKHTT.IVAALA...S.I.GIEVDTSCGE.......GV....CGTCMVDVVSGTP.....EHRD....HCLSKAERASGKV...................I.CCCVSRAR
+VANB_PSEUH/234-309 VRIHST..GQVLQVPADQT.VSQVLD...A.A.GIIVPVSCEQ.......GI....CGTCITRVVDGEP.....DHRD....FFLTDAEKAKNDQ...................F.TPCCSRAK
+VANB_PSES9/231-306 GRLARS..GLTLQVPAERS.VAQVLD...D.A.GVCIPLACEQ.......GI....CGTCLTRVLDGEP.....EHRD....SFLTDAERARNDQ...................F.TPCCSRAR
+VANB_PSEPU/231-307 VQLNST..GQVFEVPADQS.VVHVLE...Q.H.GIAIAMSCEQ.......GI....CGTCLTRVLSGTPE....ASRP....VFLTEQEQALNDQ...................F.TPCCSRSK
+VANB_ACIAD/234-309 IEVLGS..DRKIEVSAHQT.ATQALL...E.H.GFDVPVSCEQ.......GI....CGTCITRVVSGTP.....DHRD....VFMTDEEHALNDQ...................F.TPCCSRAK
+O88034_STRCO/230-305 VVLARS..GRTVAVPPGTS.VLDAVR...E.T.GVEVLYSCTE.......GT....CGTCETEVVEGEP.....DHRD....SVLTEEERAAGET...................M.LICVSRCR
+P94680_COMTE/234-309 LVLQRA..GLSTTVDAHES.VLDAME...R.V.GVDFPWSCRE.......GI....CGTCEAPVLEGEV.....QHLD....YVLSPEERAEQRR...................M.MVCVSRCG
+CBAB_COMTE/232-307 VNLARS..GAQYVVREGET.ILDVLR...N.A.GHHVTSSCRQ.......GI....CGMCETTLISGVP.....DHRD....RLLTDSEKASGRT...................M.LICCSRAL
+POBB_PSEPS/236-311 VHLARS..GRTIPIAAGCT.ILDALQ...A.G.GVAVPSSCQQ.......GV....CGICETAVLAGVP.....DHRD....LVLSDQERAAGRT...................M.MICCSGSK
+YEAX_ECOLI/237-313 LVLARS..GKEFVVPEEMT.ILQVIE...N.NKAAKVECLCRE.......GV....CGTCETAILEGEA.....DHRD....QYFSDEERASQQS...................M.LICCSRAK
+Q47914_SPHCR/241-316 VLARRS..GQEFTVEPGMT.ILETLL...Q.N.GISRNYSCTQ.......GV....CGTCETKVLEGEP.....DHRD....WVLSDEKKASNST...................M.LICCSLSK
+PDR_BURCE/241-314 VRLSRS..GTSFEIPANRS.ILEVLR...D.A.NVRVPSSCES.......GT....CGSCKTALCSGEA.....DHRD....MVLRDD..EKGTQ...................I.MVCVSRAK
+#=GR PDR_BURCE/241-314 SS EEES--..--EEEE-TTS-.HHHHHH...H.T.T-----S---.......--....----EEEEEE--E.....E---....SS--TT..T---E...................E.ETTT-EES
+PHT2_PSEPU/243-316 VTLGRS..GIDLEIPVDRS.ILEVLR...D.N.GIRAPSSCES.......GT....CGSCRTRLIEGDV.....EHRD....MVLREDEQH..DQ...................I.MICVSRAR
+O86347_MYCTU/231-301 LELARS..RRVLRVPANRS.ALDVML.....DWDPTTAYSCQQ.......GF....CGTCKVRVLAGQV.....DRRG....RIIEGDN.....E...................M.LVCVSRAV
+YFAE_ECOLI/4-77 VTLRIT..GTQLLCQDEHP.SLLAAL...E.SHNVAVEYQCRE.......GY....CGSCRTRLVAGQV......D......WIAEPLAFIQPGE...................I.LPCCCRAK
+Y1309_HAEIN/3-75 IHLIRH..NTTLEFNNET..SLLDHL...E.KNNIHHEYQCRS.......GY....CGSCRVKIKKGKV......S......YKEMPLAFIQPDE...................I.LLCCCHVE
+O31003_VIBAN/5-73 VIVKPS..GVEYQSG..RN.ILDDAF...A.S.SISLEHSCKT.......GD....CGVCCAEVISGLV.....ENEN........GELVTQG.H...................I.LTCQSKAK
+RFBI_SALTY/5-76 IKIFPS..NIEFSGREDES.ILDAAL...S.A.GIHLEHSCKA.......GD....CGICESDLLAGEVV....DSKG.........NIFGQGDK...................I.LTCCCKPK
+P95461_9PSED/17-94 VQILPQ..DVTIVLEPGQT.LLEAAL...A.N.GIAYPHDCTV.......GT....CASCKTRLKQGRVR...EATPF...GYTLSKAELDA.GY...................I.LACQAFPR
+O85971_SPHAR/13-90 VTVEGS..PTTLDIPAGKT.LLEAML...D.A.GLAMPHDCKV.......GS....CGTCKFKLVSGKIG...ELSPS...ALALEGDELRS.GF...................R.LACQAIPR
+XYLA_PSEPU/20-97 VSVRGQ..GFQFKVPRGQT.ILESAL...H.Q.GIAFPHDCKV.......GS....CGTCKYKLISGRVN...ELTSS...AMGLSGDLYQS.GY...................R.LGCQCIPK
+YCBX_ECOLI/293-362 IDWQGQ....AFRGNNQQV.LLEQLE.....NQGIRIPYSCRA.......GI....CGSCRVQLLEGEV......T.P......LKKSAMGDDGT....................ILCCSCVPK
+P96096_THIFE/9-86 HTRDKQ..QVSFVCSEAED.LLSAAD...R.G.SILLPSQCRK.......GT....CGACVATVTAGTYH...LGEVS..MEALPEKAQ.ARGDV.....................LLCRTYPR
+MMOC_METTR/7-81 ETEDGE..TCRRMR.PSED.WISR.A...E.A.ERNLLASCRA.......G.....CATCKADCTDGDYE...LIDVK..VQAVPPDEE.EDGKV.....................LLCRTFPR
+O85675_ACIAD/8-85 NFADGK..TFFIAVQEDEL.LLDAAV...R.Q.GINLPLDCRE.......GV....CGTCQGTCETGIYE...QEYVD..EDALSERDL.AKRKM.....................LACQTRVK
+BENC_ACIAD/19-98 QFEDGV..TRFIRIAQGET.LSDAAY...R.Q.QINIPMDCRE.......GA....CGTCRAFCESGNYD...MPEDNY.IEDALTPEEAQQGYV.....................LACQCRPT
+#=GR BENC_ACIAD/19-98 SS E-----..EEEEEE-----.HHHHHH...H.T.T---S-S---.......--....----EEEEEE-EEE...--GGGS.-TTT--HHHHH---E.....................ETTT-EEE
+XYLZ_PSEPU/8-86 DFEDGV..TRFIDANTGET.VADAAY...R.Q.GINLPLDCRD.......GA....CGACKCFAESGRYS...LGEE.YIEDALSEAEA.EQGYV.....................LTCQMRAE
+CBDC_BURCE/8-85 RFEDDV..TYFITSSEHET.VADAAY...Q.H.GIRIPLDCRN.......GV....CGTCKGFCEHGEYD...GGDY.I.EDALSADEA.REGFV.....................LPCQMQAR
+O66892_AQUAE/7-72 RYSDGDFRWEEYEVDGEGKTVLEILQNIKEIDPTLSFRAMCRA.......GI....CGTCVVKVN.....................GEHK..........................LACNTRVY
+O85226_PSEFL/27-86 VTA.AL..GETVLSVIQATGLRQVAR...N.DHGQLVGAYCGM.......GV....CHCCLVQIDG...................RHKR...........................RACQTLVK
+O29575_ARCFU/14-75 AYWQSFEVPAKR.GMTVLEALYYIKE...NLDSSLAFRASCRM.......GI....CGSCAMKIN.....................DKP..........................RLACETQVL
+O27878_METTH/21-82 PHLESYEIPSKE.KMKVLDALQLINK...IHGANIAFRSSCRA.......GQ....CGSCAVKMN.....................GEV..........................VLACRAEVE
+Y092_METJA/14-73 EYLESYEVP..E.NITVLEALEYINK...HYEANILFRASCRN.......AQ....CGSCAVTIN.....................GEP..........................RLACETKVE
+FER5_RHOCA/10-107 IMKKDK..TIYAVAGNTATILALAKE...H.AIPIPF..ECG........DG...DCASCLIEVTHLDN.....KPAMAMMLTEKEKARLKELQMITAEEIEAA..EVSDLPPRFRLACQFIPR
+Q44501_AZOVI/10-107 LMPHNK..KVQAVAGKRSTLLGVAQE...N.GVKIPF..ECQ........DG...NCGSCLVKITHLDG.....ERIKGMLLTDKERNVLKSVGKLPKSEEERA..AVRDLPPTYRLACQTIVT
+Q46508_DESFR/6-74 ITIDGK..TTSVPE...GSTILDAAK...T.L.DIDIPTLCYLNLEALSINNKAASCRVCVVE.....................VEGRRN....L....................APSCATPVT
+Q9ZBV9_STRCO/15-78 FTLDGQ..EARVPE...GSTILDACR...A.A.GKDVPTLCEGDT..LAPKN...ACRVCVVD.....................VEGART....L....................APACSRKAE
+NUOG_MYCTU/19-82 LTIDGV..EISVPK...GTLVIRAAE...L.M.GIQIPRFCDHPL..LEPVG...ACRQCLV.....................EVEGQR....KP....................LASCTTVAT
+O87815_CUPNE/22-85 LEVDGV..SVTVPA...GTSVMRAAM...E.A.QIAVPKLCATDS..LRNFG...SCRLCLV.....................EIEGRR....GY....................PASCTTPVE
+NQO3_THET8/4-88 VKVNDR..IVEVPP...GTSVMDAVF...H.A.GYDVPLFCSEKH..LSPIG...ACRMCLVRIGLPKKGPDGKPLLNEKGEPEIQWQP....KL....................AASCVTAVA
+#=GR NQO3_THET8/4-88 SS EE-SS-..EEEE--...--BHHHHHH...H.-.------SS--TT..S----...----SEEB-------------------------S....S-....................EETTT-B--
+P74022_SYNY3/6-69 LTIDDK..AIAIEE...GASILQAAK...E.A.GVPIPTLCHLEG..ISEAA...ACRLCMVE.....................VEGTNK....L....................MPACVTAVS
+P94157_SYNP6/6-69 LQIDDQ..ELAANV...GQTVLQVAR...E.A.SIPIPTLCHLQG..VSDVG...ACRLCVVE.....................VAGSPK....L....................QPACLLTVS
+Q44513_ANAVA/6-69 LTINDQ..LISAQE...EETLLQAAQ...E.A.GIHIPTLCHLEG..VGDVG...ACRLCLVE.....................VAGSNK....L....................LPACVTKVA
+P77908_MOOTH/4-67 LTIDGQ..RVTAPE...GMTILEVAR...E.N.GIHIPTLCHHPK..LRPLG...YCRLCLVD.....................IEGAAK....P....................MTACNTPVA
+Q9ZJW1_HELPJ/4-65 MNINGK..TIECQE...GQSVLEAAR...S.A.GIYIPTICYLSG..CSPTV...ACKMCMV........................EMDG...KR....................IYSCNTKAK
+O05397_BACSU/11-72 VRVDGT..EIQARA...GATILDILN...E.N.GIEYPQICHVPE..VDPIQ...TCDTCIV........................EANG...KL....................VRSCATVAE
+YJGC_BACSU/7-68 ITINGV..EMEASE...EQTVLQLLN...N.S.SIEVPQVCYHPS..LGPIE...TCDTCIV........................SING...EL....................KRSCSAELK
+NUOG_SALTI/4-72 IHVDGK....EYEVNGADN.LLQACL...S.L.GLDIPYFCWHPAL.GSVGA....CRQCAVK..................QYQNAEDTR...GR...................LVMSCMTPAT
+O66748_AQUAE/6-70 KIYIDD...VEIEAEKGKTVLQVALE..N....GIDIPYFCYHPR..LSIAG...ACRMCVVY.......................WEDINR......................LVISCNLPVQ
+NDUS1_DICDI/5-71 FKINEI..ECEVNEEKEDITILQACT...A.N.GIEIPRFCYHEK..LTIAG...NCRMCLV.....................YVTNEE....KL....................LAACGIPLD
+NQO3_PARDE/7-71 IKIDDT....IIEVDPNMT.LIQACE...M.A.GIEVPRFCYHER..LSIAG...NCRMCLVEVVGG........PPK........PA............................ASCAMQVK
+NDUS1_NEUCR/38-101 LTIDGK..KVSIEA...GSALIQACE...K.A.GVTIPRYCYHEK..LMIAG...NCRMCLV.....................EVEKVP....KP....................VASCAWPVQ
+NUOG_RICPR/4-67 LIIDGS..EIEISE...GSTVYQACI...Q.A.GKEIPHFCYHAR..LKIAG...NCRMCLV.....................EIEKSQ....KP....................VASCAMPVS
+NDUS1_SOLTU/70-133 VFVDGY..PVKIPK...GMTVLQACE...I.A.GVDIPRFCYHSR..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPAL
+NDUS1_RECAM/4-67 VFVDGL..SVEVKK...GATILQACA...Q.V.GIEIPRFCYHER..LSIAG...NCRMCLV.....................EVEKSP....KP....................VASCAMPVM
+NDUS1_BOVIN/34-97 VFVDGQ..SVMVEP...GTTVLQACE...K.V.GMQIPRFCYHER..LSVAG...NCRMCLV.....................EIEKAP....KV....................VAACAMPVM
+O52683_THEMA/3-65 IYVDGR..EVIIN..DNERNLLEALK.....NVGIEIPNLCYLS.....EASIYGACRMCLVEIN.......................GQIT........................TSCTLKPY
+Q46606_DESVU/3-71 AFINGK..EVRCEP...GRTILEAAR...E.N.GHFIPTLCELADIGHAPGT....CRVCLVE.....................IWRDKEAGPQI....................VTSCTTPVE
+HOXU_CUPNH/5-66 ITIDGK..TLTTEE...GRTLVDVAA...E.N.GVYIPTLCYLKDK.PCLGT....CRVCSVKVN.....................GN......V....................AAACTVRVS
+P72305_RHOOP/5-66 IEIDGV..TVTTEE...SRTLVDVAA...E.A.GVYIPTLCYLKGK.PSLGT....CRVCSVK.....................LNGTV..........................VAACTIRVA
+Q59261_CLOSA/4-67 IVIDEK..TIQVQE...NTTVIQAAL...A.N.GIDIPSLCYLNEC.GNVGK....CGVCAVE.....................IEGKNN....L....................ALACITKVE
+Q9ZNE4_CLOPE/4-67 IIINDK..TIEFDG...DKTILDLAR...E.N.GFDIPVLCELKNC.GNKGQ....CGVCLVE.....................QEGNDR....L....................LRSCAIKAK
+PHF1_CLOPA/4-67 IIINGV..QFNTDE...DTTILKFAR...D.N.NIDISALCFLNNCNNDINK....CEICTVE.....................VEGTG.....L....................VTACDTLIE
+Q59262_CLOAB/4-66 IILNGN..EVHTDK...DITILELAR...E.N.NVDIPTLCFLKDC.GNFGK....CGVCMVE.....................VEGKG.....F....................RAACVAKVE
+P74801_SYNY3/5-63 IHFLPD..DVTVAARVGEPILDVAER......AGVFIPTGCLM.......GS....CHACEVELG.......................DGTP.......................ICACISAVP
+XDHE_BACSU/18-77 MTVNGQ..AWEV.AAVPTTHLSDLLR...KEFQLTGTKVSCGI.......GR....CGACSILID.....................GK......L....................ANACMTMAY
+HCRC_THAAR/7-66 LTLNGR..ARED.LVPDNMLLLDYLR...ETVGLTGTKQGCDG.......GE....CGACTVLVD.....................DR......P....................RLACSTLAH
+#=GR HCRC_THAAR/7-66 SS EEE---..EEEE.EEETT-BHHHHHH...HT------------.......--....----EEEET.....................TE......E....................EEGGGSBGG
+P95635_RHOPA/15-74 LNVNGR..WRED.AVTDDMLLVDYLR...DIAGLTGVKTGCDG.......GE....CGACTVLID.....................GE......A....................APSCLVLAV
+XDHC_ECOLI/11-69 CTINGM..PFQLHAAPGTP.LSELLR...E.QGLLSVKQGCCV.......GE....CGACTVLVD....................G..TAID.........................SCLYLAA
+YAGT_ECOLI/65-124 LKVNGK..TEQL.EVDTRTTLLDTLR...ENLHLIGTKKGCDH.......GQ....CGACTVLVN.....................GR......R....................LNACLTLAV
+DCMS_HYDPS/8-67 VNVNGK..AQEK.AVEPRTLLIHFLR...EELNLTGAHIGCET.......SH....CGACTVDID.....................GR......S....................VKSCTHLAV
+Q52589_9PSED/8-67 MTVNGR..KVEE.AVEARTLLVHFLR...EKLNLTGTHIGCDT.......SH....CGACTVDVD.....................GK......S....................IKSCTHLAV
+O52837_BRAJA/6-65 LIVNGN..PVTA.NVDPRTLLVQFLR...ENLRLTGTHVGCDT.......SQ....CGACVVHLD.....................GK......A....................VKSCTTLAV
+O53709_MYCTU/5-64 MTVNGE..PVTA.EVEPRMLLVHFLR...DQLRLTGTHWGCDT.......SN....CGTCVVEVD.....................GV......P....................VKSCTMLAV
+O87682_ARTNI/8-67 VEVNGV..THAT.DVEPRRLLADFLR...DDLHLRGTRVGCEH.......GV....CGSCTVLLD.....................GQ......P....................VRSCTVLAV
+Q59128_ARTNI/14-73 VEVNGR..RRTV.AVDARETLADHLR...NDQKLTGIKLGCEH.......GV....CGACTILMD.....................GA......A....................VRSCLTLAA
+P72223_PSEPU/14-73 ATINGK..PRVF.YVEPRMHLADALR...EVVGLTGTKIGCEQ.......GV....CGSCTILID.....................GA......P....................MRSCLTLAV
+#=GR P72223_PSEPU/14-73 SS EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGGSBGG
+Q9ZBN8_STRCO/5-65 LTVNGR..PQEADDVWEGESLLYVLR...ERMGLPGSKNACEQ.......GE....CGSCTVRLD.....................GVP..........................VCSCLVAAG
+O54050_RHOCA/5-68 FLLNGE..TRRVRIEDPTQSLLELLR...A.EGLTGTKEGCNE.......GD....CGACTVMIRD.................AAGSR......A....................VNACLMMLP
+#=GR O54050_RHOCA/5-68 SS EEE---..EEEEE-S-TT-BHHHHHH...H.------------.......--....----EEEEES.................----E......E....................EETTTSBGG
+O23887_MAIZE/15-85 LAVNGK..RYEAAGVAPSTSLLEFLR...TQTPVRGPKLGCGE.......GG....CGACVVLVSK.................YDPATDEVTEFS....................ASSCLTLLH
+ALDO4_ARATH/8-78 FAVNGE..KFEVLSVNPSTTLLEFLR...SNTCFKSVKLSCGE.......GG....CGACIVILSK.................YDPVLDQVEEYS....................INSCLTLLC
+ALDO1_ARATH/23-95 FAINGQRFELELSSIDPSTTLVDFLR...NKTPFKSVKLGCGE.......GG....CGACVVLLSK.................YDPLLEKVDEFT....................ISSCLTLLC
+O30328_ACEEU/4-63 FRLNGR..EVTV.DVPGDTPLLWVIR...DEVGLTGTKFGCGI.......GM....CGACTIHIG.....................GR......A....................TRSCVTPVS
+IORA_BREDI/4-64 FILNGQ..PVRVTEVPEDAPLLWVVR...EHLKLSGTKFGCGL.......GL....CGACTVHIN.....................GE......A....................ARSCITPLS
+XDH_EMENI/39-108 FYLNGT..KVILDSVDPEITLLEYLR...G.IGLTGTKLGCAE.......GG....CGACTVVVS..........QIN.....PTTKKL....YHA..................SINACIAPLV
+O61198_CAEEL/8-78 FNVNGK..DIKEENVDPELTLAYYLR...NKLGLRGTKLGCEE.......GV....CGSCTVVLGT.................WDDSLNKAVYSA....................VNACLVPLF
+O17892_CAEEL/18-86 FYVNGK..RVEEKDVDPKMTLATYLR...DKLKLTGTKIGCNE.......GG....CGACTIMISH.................IENGE..IKHFS....................ANSCLMPVC
+XDH_DROSU/13-83 FFVNGK..KVTDTNPDPECTLLTYLR...DKLRLCGTKLGCAE.......GG....CGACTVMISR.................MDRGQHKIRHLA....................VNACLTPVC
+O17506_BOMMO/19-89 FYVNGK..KVIESSPDPEWTLLWYLR...KKLRLTGTKLGCAE.......GG....CGACTVMVSK.................YNRQENKIIHLA....................VNACLAPVC
+Q17250_BOMMO/18-88 FFVNGK..KVLESNPDPEWTLLFYLR...KKLKLTGTKYGCGE.......GG....CGACTVMVSK.................YLKNEDRINHIA....................VNACLISVC
+ADO_BOVIN/9-79 FYVNGR..KVTEKNVDPETMLLPYLR...KKLRLTGTKYGCGG.......GG....CGACTVMISR.................YNPITKKIRHYP....................ANACLTPIC
+XDH_BOVIN/8-78 FFVNGK..KVVEKNADPETTLLAYLR...RKLGLRGTKLGCGE.......GG....CGACTVM............LSK.....YDRLQDKIIHFS....................ANACLAPIC
+#=GR XDH_BOVIN/8-78 SS EEE---..EEEETT--TT-BHHHHHH...HT------------.......--....----EEE............EEE.....EETTTTEEEEEE....................EETTT-BGG
+MOP_DESGI/6-65 ITVNGI..EQNL.FVDAEALLSDVLR...QQLGLTGVKVGCEQ.......GQ....CGACSVILD.....................GK......V....................VRACVTKMK
+#=GR MOP_DESGI/6-65 SS EEE---..EEEE.EE-TTSBHHHHHH...HT------------.......--....----EEEE-.....................--......E....................EEGGG-BGG
+O53669_MYCTU/13-78 DESCGELREFTVEVNEGEVVLDVILRLQQTQTPDLAVRWNCKA.......GK....CGSCSAEIN.....................GKPR..........................LMCMTRMS
+O29566_ARCFU/5-80 TFL.PS..GKRAEVDEGKTILSAAQE...I.GEGIRS..LCGG.......KG...SCGKCL..VVVR........KGDVEILSEEAHEKFVRE..K.................GYYLACQTAVK
+O30225_ARCFU/5-84 TFE.PV..GKKVE.DEPDTILEIARR...N.GVLIRS..DCGG.......KG...VCGKCK..VVVVDY......RGSLSDITDHERKHLIEEEISK................GYRLACQARVE
+NQRF_CHLTR/46-122 NND.DS..LTKTV.DSGKTLLSSLLD...S.GIAIPS..PCGG.......KA...ACKQCK..VRIT.........KNADEPLETDRSTFSKQQLEQ................GWRLSCQTKVQ
+NQRF_HAEIN/43-119 NDD.PE..KAITL.PAGGKLLGALAS...K.GIFVSS..ACGG.......GG...SCGQCI..VKVK.........NGGGEILPTELSHINKREAKE................GYRLACQVNVK
+NQRF_VIBAL/39-115 NDD.PS..LAIVT.QPGGKLLSALAG...A.GVFVSS..ACGG.......GG...SCGQCR..VKVK.........SGGGDILPTELDHITKGEARE................GERLACQVAMK
+O84062_CHLTR/8-83 ADD......ENQEFHLEDGSSIAEV......CEHSGVPLACT........EG...VCGTCVIEVLEGA........DNLSDFSEAEYDFLGDPEDS.................NERLACQCCIK
+Q9Z8H9_CHLPN/8-83 SDD......EQQEFELEDNSEIAEP......CESMGIPFACT........EG...VCGTCVIEVLEGR........ENLSEFTEPEYDFLGEPEDS.................NERLACQCRIK
+CSMJ_CHLTE/5-82 IND......KPCNAKVGDLLLNTAK......LNKAHIGYICGG.......NG...ICQSCFVYVLEGA........ECLSEPGEDEKAFISDKLFAE................GGRLACRTTIV
+CSMI_CHLTE/5-82 IND......KTASSSVGQTIGKAAR......LNHAHVGYVCGG.......HG...LCQACYITVQEGA........DCLAPLTDVEKAFLSPRQIAA................GGRIACQATIA
+FER_TRIVA/13-90 AVKGGVKKQLKFEDDQTLFTVLTEAG.......LMSADDTCQG.......NK...ACGKCICKHVSGKV......A.A..E..DDEKEFLEDQPAN..................ARLACAITLS
+#=GR FER_TRIVA/13-90 SS EE----EEEE---TTEEHHHHHHT--.......----TTS---.......--...-----EEEEEE---......-.-..-..HHHHHHCTTS-TT..................EEEGGG-EE-
+P73774_SYNY3/7-88 LICLPD..NRLLEIDSNETILDALLK..G....DIAHISVCGG.......KA...NCSTCRIMVLDGIK.....NCSPPTSIEQALAKKLDFPFHV..................R.LACQTKLS
+FER_BUCAP/10-92 KLLLPK..GGCFECKEGETILNVALK...N.NIKLEHA..CEK.......SC...ACSTCH..CIIRKG......FLSLSGWSEKEEDVLDKAWGLE...............STSRLSCQAIIG
+O69222_AZOVI/11-93 EVHCPE..GRVVEAETGESILEAALR...N.DIEIEHA..CEM.......SC...ACTTCH..VIVRDG......FDSLEPSDELEDDMLDKAWGLE...............PESRLSCQARVG
+FER_HAEIN/10-92 EDFCPE..GMVVDAATGDN.LLEVAH...N.A.GVEIHHACDG.......SC...ACTTCHVIVREG........FDSLNETSDQEEDMLDKAWGLE...............MDSRLSCQCVVG
+FER_PSEAE/10-92 ADHCPE..GAVFEAKPGET.ILDAAL...R.N.GIEIEHACEK.......SC...ACTTCHVIVREG........LDSMEPSDELEDDMLDKAWGLE...............PDSRLSCQAVVA
+ADRX_YEAST/67-149 LKD.GS..QKTYEVCEGETILDIAQG...H.NLDMEG..ACGG.......SC...ACSTCH.VIVDPDY......YDALPEPEDDENDMLDLAYGLT...............ETSRLGCQIKMS
+ADX_PIG/71-155 NRD.GK..TLTTQGKVGDSLLDVVIE...N.NLDIDGFGACEG.......TL...ACSTCH.LIFEDHI......FEKLEAITDEENDMLDLAYGLT...............DRSRLGCQICLT
+FER2_RICPR/11-93 IND.EE..ERTVEAPIGLSILEIAHS...N.DLDLEG..ACEG.......SL...ACATCH.VMLEEEF......YNKLKKPTEAEEDMLDLAFGLT...............DTSRLGCQIILT
+O49551_ARATH/44-127 DKD.GE..EIHIKVPVGMNILEAAHE...N.DIELEG..ACEG.......SL...ACSTCHVIVMDTKY......YNKLEEPTDEENDMLDLAFGLT...............ATSRLGCQVIAK
+ETP1_SCHPO/525-592 TPE.GR..EIMIE....GN......E...E.G.......ACEG.......SV...ACSTCHVIVDPEHY.....ELLD..PPEEDEEDMLDLAFGLE...............ETSRLGCQVLLR
+#=GR ETP1_SCHPO/525-592 SS ---.--..EEEE-....--......-...-.-.......----.......--...--STT-EEE-HHHH.....HHS-..---HHHHHHHCTB----...............TTEE-----B--
+O07876_SPHSX/8-91 AAD.GR..EIETNVDIGTDLMHAGLY...N.SVPGLLG.ECSG.......GL...ACATCR.VHVPAEW......QGVLPAALPAEAELLGFCEESP...............PEARLSCQIKMT
+Q9ZAM5_SPHSX/8-91 SED.GS..ELETTVDVGVDLMHAGLY...N.SIPGILG.ECSG.......GL...ACATCR.VRVPVEW......QSILPPAFPSEAELLGFCDEAP...............PEARLSCQIKMT
+FER2_CAUCR/8-91 QHD.GA..EQVIDVKPGLTVMEGAVK...N.NVPGIDA.DCGG.......AC...ACATCH.VYVDEAW......LDKTGDKSAMEESMLDFAENVE...............PNSRLSCQIKVS
+FER6_RHOCA/7-91 EHN.GT..RHEVEAKPGLTVMEAARD...N.GVPGIDA.DCGG.......AC...ACSTCH.AYVDPAW......VDKLPKALPTETDMIDFAYEPNP..............ATSRLTCQIKVT
+#=GR FER6_RHOCA/7-91 SS ---.--..EEEEE-----BHHHHHHT...-.-------.----.......--...SS-TTE.EEE-HHH......HTTS----HHHHHHHTTSSS--T..............TTEEEGGG-B--
+P74447_SYNY3/31-113 IKLDPIDLKVAIETNDNLLSGLLGQD........LRIMKECGG.......RG...MCATCHVYITAGMES...LSPLNRREQRTLEVITTHNRYS...................R.LACQARVL
+P73171_SYNY3/7-85 SFPQTKFLPLSLEFNACLAEYLTPDN........SPILFGCRT.......GL....CGTCLVKVVGEIL......SPEAEEREILAILAPDDVQA...................R.LACQIKLT
+FER1_AQUAE/3-83 VIINGK....EFDIPKGVRFGELSHE.....IEKAGIEFGCTD.......GQ....CGVCVARVIKGMECL..NEPSEEEEETLWRVGAVDEDQR.....................LTCQLVIE
+FER4_RHOCA/7-86 TFTDVS...ITVNVPTGTRIIEMSEK......VGSGITYGCRE.......GE....CGTCMTHILEGSE.....NLSEPTALEMRVLEENLGGKD...................DRLACQCRVL
+P74283_SYNY3/5-88 FVKEQK....DIVVAQGANLREKALQNGVDIYTLKGKLMNCGG......YGQ....CGTCIVEITAGME.....NLSPKTDFENRVLRKKPDNFR.....................LACQTLVN
+PUTX_PSEPU/8-92 SHD.GT..RRELDVADGVS.LMQAAV...S.NGIYDIVGDCGG.......SA...SCATCHVYVN................EAFTDKVP.....AANEREIGMLECVTAELKPNSRLCCQIIMT
+#=GR PUTX_PSEPU/8-92 SS E--.--..EEEEE-----B.HHHHHH...H.---TTG------.......--...SSSTTEEEE-................TTTGTTS-.....---TTT---GGGSSS---TTEEEGGG-B--
+TERPB_PSESP/8-92 DEQSGE...YAVDAQDGQS.LMEVAT...Q.NGVPGIVAECGG.......SC...VCATCRIEIEDAWV......E.......IVGEANPDENDLLQSTGE........PMTAGTRLSCQVFID
+P95277_MYCTU/9-84 GYSDGT..HKTMPVRCDQT.VLDAAE.....EHGVAIVNECQS.......GI....CGTCVATCTAGRYQ....MG.R...TEGLSDVERAARKI.....................LTCQTFVT
+O05933_PSEPU/11-88 NFSDGV..SRSFDVEAGTS.ILDAAI.....ESEIPLLYQCRS.......GS....CSTCIAQLTEGEAH....TRAG..ASSTLLASEYASGQR.....................LLCLCQAQ
+DESET_MYCTU/303-373 FARSGK....SVAADAATS.LMDAGE.....GAGVQLPFGCRM.......GI....CQSCVVDLVEGHV......R.D.....LRTGQRHEPGTR....................VQTCVSAAS
+O23344_ARATH/57-131 VEHDGK..TTELEVEPDETILSKALD...S...GLDVPYDCNL.......GV....CMTCPAKLVTGTV.....DQSG....GMLSDDVVERGYT.....................LLCASYPT
+P74159_SYNY3/11-86 DRQNEK..DYSVIVSDDRYILHQAED...Q...GFELPFSCRN.......GA....CTACAVRVISGQIH....QP....EAMGLSPDLQRQGYA.....................LLCVSYAQ
+FER2_SYNP6/8-83 VIYQGQ..SQTFTADSDQS.VLDSAQ...A.A.GVDLPASCLT.......GV....CTTCAARILSGEV.....DQPD...AMGVGPEPAKQGYT.....................LLCVAYPR
+P73388_SYNY3/9-84 IQHQGQ..TYTISVPEDKT.VLQAAD...D.E.GIQLPTSCGA.......GV....CTTCAALITEGTA.....EQAD...GMGVSAELQAEGYA.....................LLCVAYPR
+FER1_HALMA/35-108 DEDYGS.....LEVNEGEY.ILEAAE...A.Q.GYDWPFSCRA.......GA....CANCAAIVLEGDI.....DM..D.MQQILSDEEVEDKNV....................RLTCIGSPD
+P74449_SYNY3/11-88 NPATGS..DVTIEVAEDEL.ILEAAE...N.Q.GLDLPYSCRA.......AS....CVACAGRLLEGTVE...HTDKG...SDFLKPEELAAGCV.....................LLCAAYAT
+FER2_NOSMU/10-85 NAAEGL..DETIEVPDDEY.ILDAAE...E.A.GLDLPFSCRS.......GS....CSSCNGILKKGTV.....DQSD...QNFLDDDQIAAGNV.....................LTCVAYPT
+FER2_APHSA/10-86 NEEEGI..NAILEVADDQT.ILDAGE...E.A.GLDLPSSCRA.......GS....CSTCAGKLVSGAA.......PNQDDQAFLDDDQLAAGWV.....................MTCVAYPT
+FER1_CYAPA/10-85 CEEQGL..DTTIECPDDEY.ILDAAE...E.Q.GIDLPYSCRA.......GA....CSTCAGKVVEGTV.....DQSD...QSFLDDAQLAAGYV.....................LTCVAYPS
+FER_PORPU/10-85 SEDEGI..DVTFDCSEDTY.ILDAAE...E.A.GIELPYSCRA.......GA....CSTCAGKVTEGSV.....DQSD...QSFLDDEQLLKGYV.....................LTCIAYPE
+FER_ODOSI/10-85 SEEHDI..DATIDCNDDVF.LLDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVTEGDI.....DQSE...QTFLDDDQVGAGFV.....................LTCIAYPK
+FER_BUMFI/9-84 NEEKNI..NAVIKCPDDQF.ILDAAE...E.Q.GIELPYSCRA.......GA....CSTCAGKVLSGTI.....DQSE...QSFLDDDQMGAGFL.....................LTCVAYPT
+FER3_CYACA/9-84 NKDQGI..DETIECPDDQY.ILDAAE...E.Q.GLDLPYSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQVKAGFV.....................LTCVAYPT
+FER2_CYACA/8-83 NQKEGV..DVTINCPGDQY.ILDAAE...E.Q.GVDLPYSCRA.......GA....CSTCAGKLVKGSV.....DQSD...QSFLDEEQINNGFI.....................LTCVAYPT
+FER_BRYMA/8-83 KLDDGS..EAVIDCDEDSF.ILDVAE...E.E.GIDIPFSCRS.......GS....CSTCAGKIEGGTV.....DQSE...QTFLDDDQMEEGYV.....................LTCVAYPT
+FER_APHSA/9-83 KTPDGD..NVIT.VPDDEY.ILDVAE...E.E.GLDLPYSCRA.......GA....CSTCAGKLVSG........PAPDEDQSFLDDDQIQAGYI.....................LTCVAYPT
+FER_THEVL/9-84 VRPDGS..ETTIDVPEDEY.ILDVAE...E.Q.GLDLPFSCRA.......GA....CSTCAGKLLEGEV.....DQSD...QSFLDDDQIEKGFV.....................LTCVAYPR
+FER_PERBI/6-80 DTPDGK...KSFECPGDSY.ILDKAE...E.E.GLELPYSCRA.......GS....CSSCAGKVLTGSI.....DQSD...QAFLDDDQGGDGYC.....................LTCVTYPT
+FER3_RAPSA/8-82 ITPEGE...QEVECDDDVY.VLDAAE...E.A.GIDLPYSCRA.......GS....CSSCAGKVVSGSV.....DQSD...QSFLDDDQIAEGFV.....................LTCAAYPT
+FER1_SPIOL/58-132 VTPTGN...VEFQCPDDVY.ILDAAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLKTGSL.....NQDD...QSFLDDDQIDEGWV.....................LTCAAYPV
+FER_SILPR/57-131 TKESGT...VTFDCPDDVY.VLDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVVAGSV.....DQSD...QSFLDDDQIEAGWV.....................LTCAAYPS
+FER_WHEAT/54-128 VTPEGE...VELEVPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKLVSGEI.....DQSD...QSFLDDDQMEAGWV.....................LTCHAYPK
+FER_SAMNI/8-82 ITPDGP...QEFECPDDVY.ILEHAE...E.L.GIDIPYSCRA.......GS....CSSCAGKLVAGSV.....DQSD...QSFLDDEQIEEGWV.....................LTCVAYPK
+FERA_ALOMA/8-82 VTPQGQ...QEFDCPDDVY.ILDQAE...E.E.GIDLPYSCRA.......GS....CSSCAGKVKQGEV.....DQSD...GSFLDDEQMEQGWV.....................LTCVAFPT
+FER_ARCLA/8-82 ITPEGK...QEFEVPDDVY.ILDHAA...E.E.VGDLPYSCRA.......GS....CSSCAGKVTAGSV.....DQSD...GSYLDDDQMEAGWV.....................LTCVAYPT
+FER_DATST/8-82 VTPDGP...VEFNCPDDVY.ILDQAE...E.E.GHDLPYSCRA.......GS....CSSCAGKVTAGTV.....DQSD...GNYLDDDQMADGFV.....................LTCVAYPQ
+FER_PALPL/9-83 STPGGV...EEIEGDETTY.VLDSAE...D.Q.GIDLPYSCRA.......GA....CSTCAGIVELGTV.....DQSD...QSFLDDDQLNDSFV.....................LTCVAYPT
+FER_EUGVI/8-82 INPDGE..VTI.ECGEDQY.ILDAAE...D.A.GIDLPYSCRA.......GA....CSSCTGIVKEGTV.....DQSD...QSFLDDDQMAKGFC.....................LTCTTYPT
+FER_CHLFU/6-80 KTPSGE...ETIECPEDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSSCAGKVESGEV.....DQSD...QSFLDDAQMGKGFV.....................LTCVAYPT
+FER_SYNY4/9-83 ITPDGE...NSIECSDDTY.ILDAAE...E.A.GLDLPYSCRA.......GA....CSTCAGKITAGSV.....DQSD...QSFLDDDQIEAGYV.....................LTCVAYPT
+FER1_PHYAM/8-82 VTPSGT...QTIDCPDDTY.VLDAAE...E.A.GLDLPYSCRA.......GS....CSSCTGKVTAGTV.....DQED...QSFLDDDQIEAGFV.....................LTCVAFPK
+FER2_PHYAM/9-83 VTPSGT...NTITCPADTY.VLDAAE...E.S.GLDLPYSCRA.......GA....CSSCAGKVTAGAV.....NQED...GSFLEEEQMEAGWV.....................LTCVAYPT
+FER2_SPIOL/8-82 VTPSGS...QVIECGDDEY.ILDAAE...E.K.GMDLPYSCRA.......GA....CSSCAGKVTSGSV.....DQSD...QSFLEDGQMEEGWV.....................LTCIAYPT
+FER_PHYPA/57-132 DGETGA..ENVXECSDEEY.XLDAAE...R.A.GMDLPYSCRA.......GA....CSSCAGIIKAGEV.....DQSD...QSFLDDSQIDDGFV.....................LTCVAYPA
+FER_MARPO/7-81 NTPTGQ...SVIDVEDDEY.ILDAAE...E.A.GLSLPYSCRA.......GA....CSSCAGKVTAGEV.....DQSD...ESFLDDDQMDEGYV.....................LTCIAYPT
+#=GC SS_cons EEESS-EEEEEEEEEETTCBHHHHHH...HTT-TTTGTTSS--TT..S..--...SSSTTEEEEEEHCEE....EHCCS..TTHHHHHHHTTSSET-TTT---GGGSSS---TTEEECCCSBGG
+#=GC seq_cons hphsup..thphpsssspp.lLcshc...p.t.slslshuCps.......Gs....CusCtsplhtu.................hpspphttt.h.....................LuCtshsp
+//
--- /dev/null
+# STOCKHOLM 1.0
+
+#=GF ID SECIS_1
+#=GF AC RF00031
+#=GF DE Selenocysteine insertion sequence 1
+#=GF AU Griffiths-Jones SR
+#=GF GA 20.0
+#=GF NC 0.0
+#=GF TC 22.6
+#=GF PI SECIS
+#=GF SE Gautheret D, PMID:12458087
+#=GF SS Published; PMID:12458087
+#=GF TP Cis-reg;
+#=GF BM cmbuild -F CM SEED; cmcalibrate --mpi -s 1 CM
+#=GF BM cmsearch -Z 169604 -E 1000 --toponly CM SEQDB
+#=GF DR SO:1001274 SO:SECIS_element
+#=GF DR GO:0001514 GO:selenocysteine incorporation
+#=GF RN [1]
+#=GF RM 8634917
+#=GF RT A novel RNA structural motif in the selenocysteine insertion element
+#=GF RT of eukaryotic selenoprotein mRNAs.
+#=GF RA Walczak R, Westhof E, Carbon P, Krol A;
+#=GF RL RNA 1996;2:367-379.
+#=GF RN [2]
+#=GF RM 12458087
+#=GF RT A survey of metazoan selenocysteine insertion sequences.
+#=GF RA Lambert A, Lescure A, Gautheret D;
+#=GF RL Biochimie 2002;84:953-959.
+#=GF CC The incorporation of selenocysteine into a protein sequence
+#=GF CC is directed by an in-frame UGA codon (usually a stop codon)
+#=GF CC within the coding region of the mRNA. Selenoprotein mRNAs
+#=GF CC contain a conserved secondary structure in the 3' UTR that
+#=GF CC is required for the distinction of UGA stop from UGA
+#=GF CC selenocysteine. The selenocysteine insertion sequence
+#=GF CC (SECIS) is around 60 nt in length and adopts a hairpin
+#=GF CC structure which is sufficiently well-defined and conserved
+#=GF CC to act as a computational screen for selenoprotein genes [2].
+#=GF WK http://en.wikipedia.org/wiki/SECIS_element
+#=GF SQ 61
+
+#=GS D.melanogaster.1 AC AY119185.1/838-902
+#=GS D.melanogaster.2 AC AC092237.1/57223-57161
+#=GS D.melanogaster.3 AC AY060611.1/560-627
+#=GS O.niloticus.1 AC Y11109.1/1272-1330
+#=GS O.niloticus.2 AC Y11109.1/927-987
+#=GS O.niloticus.3 AC Y11111.1/1260-1324
+#=GS D.rerio.1 AC AF322071.1/1577-1642
+#=GS X.laevis.1 AC L28111.1/1299-1365
+#=GS G.gallus.1 AC AF125575.1/5781-5843
+#=GS G.gallus.2 AC Y11110.1/1218-1277
+#=GS G.gallus.3 AC Y11273.1/1139-1211
+#=GS M.musculus.1 AC AF195142.1/461-524
+#=GS M.musculus.2 AC AF021345.1/10097-10160
+#=GS M.musculus.3 AC X03920.1/1172-1235
+#=GS M.musculus.4 AC AF096875.1/5504-5568
+#=GS M.musculus.5 AC AF241527.2/359-424
+#=GS M.musculus.6 AC AF136399.1/1808-1868
+#=GS M.musculus.7 AC X84742.1/5239-5302
+#=GS M.musculus.8 AC AF288740.1/1291-1357
+#=GS M.musculus.9 AC AF274027.1/835-900
+#=GS M.musculus.10 AC AB030643.1/4176-4241
+#=GS M.musculus.11 AC AL645723.11/192421-192359
+#=GS M.musculus.12 AC AC002327.1/156204-156268
+#=GS M.musculus.13 AC AF333036.1/2190-2249
+#=GS M.musculus.14 AC U43285.1/2009-2075
+#=GS R.norvegicus.1 AC X57999.1/1526-1586
+#=GS R.norvegicus.2 AC M63574.1/1465-1528
+#=GS R.norvegicus.3 AC AF390544.1/1076-1142
+#=GS R.norvegicus.4 AC AF072865.1/1887-1947
+#=GS R.norvegicus.5 AC X12367.1/703-764
+#=GS R.norvegicus.6 AC U25264.1/366-432
+#=GS R.norvegicus.7 AC L24896.1/600-665
+#=GS H.sapiens.1 AC AF201385.1/3055-3117
+#=GS H.sapiens.2 AC AL049837.4/130674-130738
+#=GS H.sapiens.3 AC U67171.1/375-442
+#=GS H.sapiens.4 AC AF195141.1/689-759
+#=GS H.sapiens.5 AC X53463.1/847-903
+#=GS H.sapiens.6 AC AF093774.1/5851-5916
+#=GS H.sapiens.7 AC X58295.1/1384-1453
+#=GS H.sapiens.8 AC AL833145.1/1479-1545
+#=GS H.sapiens.9 AC S48220.1/1731-1788
+#=GS H.sapiens.10 AC X71973.1/730-791
+#=GS H.sapiens.11 AC AF166127.1/1919-1981
+#=GS H.sapiens.12 AC U43286.1/2054-2120
+#=GS H.sapiens.13 AC BC003127.1/865-928
+#=GS H.sapiens.14 AC S79854.1/1605-1666
+#=GS H.sapiens.15 AC X13710.1/946-1008
+#=GS B.taurus.1 AC D88033.3/5711-5774
+#=GS B.taurus.2 AC D25220.1/1493-1556
+#=GS B.taurus.3 AC AB017534.1/661-726
+#=GS B.taurus.4 AC AB032826.1/1401-1464
+#=GS B.taurus.5 AC AB022283.1/1669-1729
+#=GS B.taurus.6 AC AF053984.1/1951-2017
+#=GS B.taurus.7 AC X13684.1/700-760
+#=GS O.aries.1 AC U67853.1/375-442
+#=GS S.scrofa.1 AC AF380118.1/366-433
+#=GS S.scrofa.2 AC L12743.1/694-758
+#=GS S.scrofa.3 AC AF532927.1/678-740
+#=GS S.scrofa.4 AC X76008.1/2709-2772
+#=GS C.elegans.1 AC U61947.2/4246-4309
+#=GS S.mansoni.1 AC L37762.1/2940-3006
+
+D.melanogaster.1 G.AGCC.CU...AUGAUCGAUGAUUGG.CAAA.UCCUCUC..GAGG..A.......ACCGAUC.G.U.UGAGAA..CCCCU.....UUGCCUU
+#=GR D.melanogaster.1 SS ................(((((((((((......((((......)))..)........)))))).).).)))......................
+D.melanogaster.2 C.AUUCAACU.UAUGAGGAUUAUUUCU.UAAA.GGCCUCU...GGC..U.......CGGAAAU.A.G.UCUGAA...CCU........UAUUG
+#=GR D.melanogaster.2 SS ................(((((((((((......((((......)))..)........)))))).).).)))......................
+D.melanogaster.3 G.UGGCGCU..UAUGACGCAGUUGUCU.UAAA.CUCGAAC..UCGA.GC........GGGCAA.U.U.GCUGAU...UACG...AUUAACCAC
+#=GR D.melanogaster.3 SS (.(((...(....((((((((((((((......((((......))).).........)))))).).).)).).)...)).....)....))))
+O.niloticus.1 G.UUUCUCA...GUGAAGGCUACAGAU.UAAA..CCUCU....GGC...........CUCUGG.A.G.CCAGAU..GCAUU.......GAAAC
+#=GR O.niloticus.1 SS ......(((...(((..(((((.((..........)).)....)))...........)((((.......))))....)))).......))...
+O.niloticus.2 U.GUUUAUU..AAUGACGGCUACAGAU.UAAA..CCUUU....AGC...........CUCUGG.A.G.CCAGAU..GCAUU......CAAACA
+#=GR O.niloticus.2 SS ..((((.....((((..(((((.((..........)).)....)))...........)((((.......))))....)))).......)))).
+O.niloticus.3 G.UGUCUCU...GUGAAGUUCGGUUUU.UAAA.AGGGUCA...UCC..A.......GAAAACC.G.ACACUGAU..GUUUC......CGACAC
+#=GR O.niloticus.3 SS (.((((..........(((((((((((.(......((.......))..........))))))).).).))).................)))))
+D.rerio.1 A.UGUGGUCUUUAUGAAGGCAGGUGCA.GAAA.CUAUGCA...CUA.GU........GGUGUC.U.G.UCUGAU..GUUUG.......GCCAU
+#=GR D.rerio.1 SS ...((((((.......(((((((..(.....(.(((........)).)).........)..)).).).))).........).......)))))
+X.laevis.1 G.UGUUUGCA.AAUGACGACCGAUUUU.GAAA.UGGUCUCACGGCC..A.......AAAACUC.GUG.UCCGAC...AUC........AACCC
+#=GR X.laevis.1 SS .................((((((.(((......(((((....))))..)........))).)).).).)).......................
+G.gallus.1 G.UGUGUUU...AUGAAGAGCACUAAC.AAAA.GAGUAAU.UGACU..C.......AGUUGGU.G.U.UCAGAU..GCU.........CUCAC
+#=GR G.gallus.1 SS (.((.(..(...((...((((((((((......((((......)))..)........)))))).).).))..))..)...........).)))
+G.gallus.2 U.AUUUGUC...AUGACAGUCACAGCA.UAAA..GCGCA....GAC...........GGCUGU.G.A.CCUGAU..UUUAG......AAAAUA
+#=GR G.gallus.2 SS ................((((((((((................................))))).).)..))).....................
+G.gallus.3 U.AUUUCUU..UGUGAUGACCGAUUUU.GAAA.UGGGUUU...CUC..UAAUGCCAGGAAAUC.GUG.UCUGAU...GUUG.....UCAAGUA
+#=GR G.gallus.3 SS ......(((...(..((((((((((((......((((((..........))).))).)))))).).).)).......)).......).)))..
+M.musculus.1 G.UCACCGA...AUGAUCUGCUCUGGU.CAAA.UCCUUCU...AUG..C......CAGCCAGG.G.U.GGUGAU..GACCC.......GUGAC
+#=GR M.musculus.1 SS (.((((.(....((.(((.((((((((..............................)))))).).).))).)).....)........)))))
+M.musculus.2 G.UUACAUU..AAUGAGAACAGAAACA.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU..AGCUU.......GUAAU
+#=GR M.musculus.2 SS (.(((((..........(((((((((........(((......)))............))))).).).))..........).......)))))
+M.musculus.3 G.GUUCUUC..CAUGAUGGUGUUUCCUCUAAA..UUUGC....ACG...........GAGAAA.C.A.CCUGAU.UUCCAG.....GAAAAUC
+#=GR M.musculus.3 SS (.(((.(((..(..((.((((((((.(((................)...........)))))).).).))......))..).....)))))))
+M.musculus.4 G.UGUGCGA...AUGAUAACUACUGAC.GAAA.GAGCUGU.CUGCU..C.......AGUCUGU.G.G.UUGGAU...GUAG......UCACAC
+#=GR M.musculus.4 SS (.(((((.........(((((((.(((......((((......)))..)........))).)).).).))).........).......)))))
+M.musculus.5 G.CCGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUUA...GAC..C.....UGUGGUCUU.U.C.CUCGAU..GUUCC......UGCGGC
+#=GR M.musculus.5 SS (.((((..(...((...((((((((((.(.....(((......)))..........))))))).).).))..))..)...........)))))
+M.musculus.6 G.UCAGAUG...AUGAUGGCCUGGGCA.GAAA.CCCCAUG..UGGG..C........CGCCCA.G.G.UUUGAA...CCC........CUGGC
+#=GR M.musculus.6 SS (.((((...........(((((((((..(.....(((......)))..).........))))).).).))..................)))))
+M.musculus.7 G.UGUCUCU...AUGAAGGAGGGGCCC.GAAG.CCCUUGU...GGG..C........GGGCCU.C.C.CCUGAG...CCCG....UCUGUGGU
+#=GR M.musculus.7 SS ................(((.(((((((....(.(((.......)))..)........)))))).)...)))..(...(((........).)))
+M.musculus.8 U.UUGCAUU..AAUGAGGAUUACACAG.AAAA.CCUUUGU..UAAG.GA.......CUUGUGU.AGA.UCUGAU..AAUUG.......GCAAA
+#=GR M.musculus.8 SS ..((((......((.(((.((((((((......((((......))).).........)))))).))..))).))..............)))).
+M.musculus.9 C.CGGCACU..CAUGAAGGUCUGCUUG.AAAA.CCAGCCU..GCUG.GU........GGGGCA.G.U.CCUGAG.GACCUG.......GCGUG
+#=GR M.musculus.9 SS (.(((..((..((....((.((((((.....(.((((......))).)).........))))).)...))))))...)).).......)....
+M.musculus.10 C.CGGCACU..CAUGAAGGUCUGCCUG.AAAA.CCAGCCU..GCUG.GU........GGGGCA.G.U.CCUGAG.GACCUG.......GCGUG
+#=GR M.musculus.10 SS (.(((..((..((....((.((((((.....(.((((......))).)).........))))).)...))))))...)).).......)....
+M.musculus.11 U.AUUUGUG..UAUGAUGGUCACAGUG.UAAA..GUUCC....CAC...........AGCUGU.G.A.CUUGAU..UUUUA....AAAAUGUC
+#=GR M.musculus.11 SS (.((((...........((((((((((.(...............))...........).)))).).).))................)))))..
+M.musculus.12 C.UCAGCAG..GAUGAUGAGAAGGGCU.GAAA.UGCUGCC..AAAC..C.......AGGUCCU.U.U.UCUGAU..GGUGG.......CUGGG
+#=GR M.musculus.12 SS (.(((((..........((((((((((......((....)..)..............)))))).).).))..........).......)))))
+M.musculus.13 C.AUGCGUC..CAUGAAGUCACUGGCC.UCAA.GCCCAA....GUG.GU........GGGCAG.U.G.ACAGAA...GA.........GCUGC
+#=GR M.musculus.13 SS (.(((......))))..(((((((.((......(((.........).))........)).))).).).)).......................
+M.musculus.14 C.UCUGAUA...AUGAUGUCUCUCCCU.CUAA.CUCCCAGUAAGGA..C........UGGGAG.A.G.GCUGAACAAACCU.......CAGAG
+#=GR M.musculus.14 SS (.(((((.........(((.((..(((.(.....(((((((....)..)........)))))).).).)..)))))....).......)))))
+R.norvegicus.1 A.UAUUUGUU.UAUGAUGGUCACAGUG.UAAA..GUUCA....CAC...........AGCUGU.G.A.CUUGAU..UUUUA.......AAAAU
+#=GR R.norvegicus.1 SS ....((((.........((((((((((.(...............))...........).)))).).).)).........)).......))...
+R.norvegicus.2 G.UUACAUU..GAUGAGAACAGAAACA.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU..AGCUC.......GUAAU
+#=GR R.norvegicus.2 SS ............((((((((((((((........(((......)))............))))).).).))........))).......))...
+R.norvegicus.3 U.UUGCAUU..AAUGAGGAUUACACAG.AAAA.CCUUUGU..UAAGGGU........UUGUGUCG.A.UCUGCU..AAUUG.......GCAAA
+#=GR R.norvegicus.3 SS ..((((..........(((((((((((.(....((((......)))).)........)))))).).).))).................)))).
+R.norvegicus.4 G.UCAGAUG...AUGACGGCCUGUGCA.GAAA.CCCCCAC.GUGGG..C........UGC.CA.G.G.UUUGAA...CCC........CUGGC
+#=GR R.norvegicus.4 SS (.(((........)))).(((..((...(.......)..).)..))..).........((.((.(.(............)........)))))
+R.norvegicus.5 G.UUUUUCC...AUGACGGUGUUUCCUCUAAA..UUUAC....AUG...........GAGAAA.C.A.CCUGAU.UUCCAG......AAAAAU
+#=GR R.norvegicus.5 SS (.((((((......(((((((((((.((((..............))...........)))))).).).)).).).)....)......))))))
+R.norvegicus.6 G.CCGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUCA.AAGAC..C.....UGUGGUCUU.U.C.UUCGAU..GUUCU.......GCGGC
+#=GR R.norvegicus.6 SS (.((((..(...((((..(((((((((.(.....(((......)))..........))))))).).).))).))..)...........)))))
+R.norvegicus.7 C.CGGCACU..CAUGACGGUCUGCCUG.AAAA.CCAGCCC..GCUG.GU........GGGGCA.G.U.CCCGAG.GACCUG.......GCGUG
+#=GR R.norvegicus.7 SS (.(((..((..(.....((.((((((.....(.((((......))).)).........))))).)...)).)))...)).).......)....
+H.sapiens.1 G.CCAGAUG...AUGACGACCUGGGUG.GAAA.CCUACCC.UGUGG..G........CACCCA.U.G.UCCGAG...CCCC.......CUGGC
+#=GR H.sapiens.1 SS (.((((...........(((.((((((......(((((....))))..)........))))))...).))..................)))))
+H.sapiens.2 G.UGUGCGG...AUGAUAACUACUGAC.GAAA.GAGUCAU.CGACU..C.......AGUUAGU.G.G.UUGGAU...GUAG......UCACAU
+#=GR H.sapiens.2 SS (.(((((.........(((((((((((......(((((....))))..)........)))))).).).))).........).......)))))
+H.sapiens.3 G.ACGCUUC...AUGAUAGGAAGGACU.GAAA.AGUCUUG.UGGAC..A.....CCUGGUCUU.U.C.CCUGAU..GUUCU......CGUGGC
+#=GR H.sapiens.3 SS ..(((...(...((.(..(((((((((.......(((......)))...........)))))).).).).).))..)..........)))...
+H.sapiens.4 G.ACUGACAU.UAUGAAGGCCUGUACU.GAAG.ACAGCAA..GCUG..U.......UAGUACA.G.A.CCAGAU..GCUUU..CUUGGCAGGC
+#=GR H.sapiens.4 SS ...(((.((.....(((((((((((((....(.((((......)))..).......))))))).)...........)))))..).)).)))..
+H.sapiens.5 U.UCACAGA...AUGAUGGCACCUUCC.UAA...ACCCU....CAU...........GGGUGG.U.G.UCUGAG..AGGC........GUGAA
+#=GR H.sapiens.5 SS ..((((...........((((((...........((((...................)))))).).).))..................)))).
+H.sapiens.6 G.UGUGCGG...AUGAUAACUACUGAC.GAAAGAGUCAUC...GAC..C.....UCAGUUAGU.G.G.UUGGAU...GUAG......UCACAU
+#=GR H.sapiens.6 SS (.(((((.........(((((((((((....((.(((......)))..).....)..)))))).).).))).........).......)))))
+H.sapiens.7 U.GGCGUCUU.CAUGAGGGAGGGGCCC..AAA.GCCCUUG..UGGG..C........GGACCU.C.C.CCUGAG...CCUGUCUGAGGGGCCA
+#=GR H.sapiens.7 SS ..(((.((((.((...((((((((.........((((......)))..)...............).).)))......)))...))))))))).
+H.sapiens.8 U.UUGCUUU..AAUGAGAAUAGAAACG.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU.AAUUAG.....CAGUUUA
+#=GR H.sapiens.8 SS ..(((((..........(((((((((........(((......)))............))))).).).)).........)).....)))....
+H.sapiens.9 U.AUUUGUU..UAUGAUGGCCACAGCC.UAAA..GUACA....CAC...........GGCUGU.G.A.CUUGAU...UCA........AAAGA
+#=GR H.sapiens.9 SS .............(((.((.(((((((..............................)))))).)...)).......))).............
+H.sapiens.10 C.CGGCACU..CAUGACGGCCUGCCUG.CAAA..CCUGC....UGG..U........GGGGCA.G.A.CCCGAA.AAUCCA.......GCGUG
+#=GR H.sapiens.10 SS ...((((....(......)..))))............((....(((..(........(((........))))......))).......))...
+H.sapiens.11 G.CCGGAUG...AUGACGACCUGGGUG.GAAA.CCUACCC.UGUGG..G........CACCCA.U.G.UCCGAG...CCCC.......CUGGC
+#=GR H.sapiens.11 SS (.((((...........(((.((((((......(((((....))))..)........))))))...).))..................)))))
+H.sapiens.12 C.UCUGUUA...AUGACGUCUCUCCCUCUAAA.CCCCAUU.AAGGA..C........UGGGAG.A.G.GCAGAGCAAGCCU.......CAGAG
+#=GR H.sapiens.12 SS (.((((.......((..(((((((((.......((........)).............))))).).).))....))............)))))
+H.sapiens.13 G.UCACUGC...AUGAUCCGCUCUGGU.CAAA.CCCUUCC...AGG..C......CAGCCAGA.G.U.GGGGAU..GGUCU.......GUGAC
+#=GR H.sapiens.13 SS (.((((.((.......(((((((((((......((.........))...........)))))).).).)))......)).........)))))
+H.sapiens.14 C.ACUGCUG...AUGACGAACUAUCUC.UAAC.UGGUCUU..GACC..A.......CGAGCUA.G.U.UCUGAA...UU.G.......CAGGG
+#=GR H.sapiens.14 SS ...((((.(...((...((((((.(((......((((......)))..)........))).)).).).))...)...)).).......)))..
+H.sapiens.15 U.UUUCAUC..UAUGAGGGUGUUUCCUCUAAA..CCUACG...AGG...........GAGGAA.C.A.CCUGAU...CUUA.....CAGAAAA
+#=GR H.sapiens.15 SS .......((..(.((((((((((.(((((................)...........)))))).).).)).......))))......)))...
+B.taurus.1 C.UUGCGUU..AAUGAGAACAGAAACG.UAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAAC
+#=GR B.taurus.1 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))...
+B.taurus.2 C.UUGCGUU..AAUGAGAACAGAAACG.AAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAAC
+#=GR B.taurus.2 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))...
+B.taurus.3 C.CCGGUGCC.UAUGACGGUCUGUCUG.AAAA.CCAGCCC...CUG.GU........GGGGCA.G.A.CCUGAG.AACCUG.......GCGUG
+#=GR B.taurus.3 SS (.(.(((..(.(.....(((((((((.....(.((((......))).)).........))))).).).))..))..))).).......)....
+B.taurus.4 ACUUGCGUU..AAUGAGAACAGAAACG.UAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAA.
+#=GR B.taurus.4 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))...
+B.taurus.5 G.CCAGAUG...AUGAGGACCUGUGCG.GAAA.CCCCCCG..CGGG..C........UGCCCA.U.G.UCUGAG...CCC........CUGGC
+#=GR B.taurus.5 SS (.((((((....(((.((.((((((.(.(.......))))..)))).............)))).).).)))).)...)...............
+B.taurus.6 G.AUGCGUC..CAUGAAGUCACCAGCC.CCAA.GCCCCUC...GUG.GU........GGGUGG.U.G.AUGGAA.CCGUCA.....AAGCAGU
+#=GR B.taurus.6 SS (.(((..((..((.....((((((.((.(((.............)).).........)).))).).).)))))...)))).............
+B.taurus.7 U.UUUGCCC...AUGAAGGUGUUCCCUCUAAA..CCUAC....GUG...........GAGGAA.U.G.CCUGAU.GUCCAG.......GAAAA
+#=GR B.taurus.7 SS (.((((..(...((..(((((((((.((((..............))...........)))))).).).))).)).)..))).......))...
+O.aries.1 G.ACGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUCU.UGGAC.GC......CUGGUCCU.U.C.CUUGAU..GUUCU......CACGGC
+#=GR O.aries.1 SS (.(.((.((...(....((((((((((.(....((((......))).)........))))))).).).)))))...))..)......).....
+S.scrofa.1 G.ACGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUUG.UGGAC.GC......CUGGUCCU.U.C.CCUGAU..GUUCU......CAUGGC
+#=GR S.scrofa.1 SS .......((...(((((((((((((((.(....((((......))).)........))))))).)...))))........)......))))).
+S.scrofa.2 C.UGGCACC..CAUGACAGUCUGCCUA.AAAA.CCAGCCC...CUG.GU........GGGGCA.G.A.CUCGAG.AACCUG.......GCGUG
+#=GR S.scrofa.2 SS .....((((..((.(.((((((((((.....(.((((......))).)).........))))).).).)).).....).)).......).)))
+S.scrofa.3 A.UUUUAUC..CAUGAAAGUGUUUCCUCUAAA..CCUAU....GUG...........GAGGAA.C.A.CCUGAU.GUCCAG......GAAAAU
+#=GR S.scrofa.3 SS ...........(((....))).((((((((..............))...........)))))).....((((......)))......).....
+S.scrofa.4 C.UGGCACC..CAUGACAGUCUGCCUA.AAAA.CCAGCC....CUG.GU........GGGGCA.G.A.CUCGAG.AACCUG.......GCGUG
+#=GR S.scrofa.4 SS .....((((..((.(.((((((((((.....(.(((........)).)).........))))).).).)).).....).)).......).)))
+C.elegans.1 G.AGGCAGCUUUGUGACGACCUUUGGC.UAAA.CUCCAUC..GUGA.GC........GCCUCU.G.G.UCUGAU...GC.........GCCUC
+#=GR C.elegans.1 SS (.((((.((...((.(.((((...(((......(((........)).).........)))....).).))).))...)).........)))))
+S.mansoni.1 C.UCGCUAU...AUGACGAUGGCAAUC.UCAA..AUGUU....CAU..U........GGUUGC.C.A.UUUGAU..GAAAUCAGUUUUGUGUG
+#=GR S.mansoni.1 SS ...(((.((...(.(((((((((((((..............................)))))).).).)).............))).))))))
+#=GC SS_cons <-<<<<-----------<<<<<<<<<<-------<<<______>>>----------->>>>>>->->->>------------------>>>>>
+#=GC RF g.ucucauu..uAUGAuGgccucuccc.uAAA.ucccuuu...ggg..c........gggaga.g.g.cCuGAU..gcuug.......gagac
+//
--- /dev/null
+#nav #navInner
+{
+margin-top:0x;
+}
+
+
+#sddm
+{
+ position:relative;
+ top:0;
+}
+
+
+#sddm li a.download-right
+{
+position:absolute;
+top:28px;
+left:270px;
+}
+
+#sddm li
+{
+padding-top:30px;
+padding-bottom:30px;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ top:80px;
+ z-index:9999;
+ width:0;
+ display:none;
+}
+
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: left;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ z-index:100;
+ left:-1100px;
+ }
+
+
+#nav
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
+
+#content
+{
+position:relative;
+z-index:2;
+ clear:both;
+ float:left;
+ width:100%; /* width of whole page */
+}
--- /dev/null
+#sddm\r
+{\r
+ position:relative;\r
+ top:0;\r
+}\r
+\r
+\r
+#sddm li a.download-right\r
+{\r
+position:relative;\r
+left:0;\r
+}\r
+\r
+#sddm li\r
+{\r
+padding-top:30px;\r
+padding-bottom:30px;\r
+}\r
+\r
+#sddm div\r
+{ position: absolute;\r
+ visibility: hidden;\r
+ margin: 0;\r
+ padding: 0;\r
+ background: #555;\r
+ border: 1px solid #000000;\r
+ top:80px;\r
+ z-index:9999;\r
+ width:120px;\r
+}\r
+\r
+\r
+ #sddm div a\r
+ { position: relative;\r
+ display: block;\r
+ margin: 0;\r
+ padding:8px;\r
+ width: 200px;\r
+ white-space: nowrap;\r
+ text-align: left;\r
+ text-decoration: none;\r
+ background: #555;\r
+ color: #fff;\r
+ border: 1px solid #000000;\r
+ background: #555;\r
+ z-index:100;\r
+ left:-80px;\r
+ }\r
+ \r
+ \r
+#nav\r
+{\r
+position:relative;\r
+z-index:2;\r
+ clear:both;\r
+ float:left;\r
+ width:100%; /* width of whole page */\r
+}\r
+\r
+#content \r
+{\r
+position:relative;\r
+z-index:2;\r
+ clear:both;\r
+ float:left;\r
+ width:100%; /* width of whole page */\r
+}\r
--- /dev/null
+/* http://meyerweb.com/eric/tools/css/reset/
+
+ v2.0 | 20110126
+
+ License: none (public domain)
+
+*/
+
+
+
+html, body, div, span, applet, object, iframe,
+
+h1, h2, h3, h4, h5, h6, p, blockquote, pre,
+
+a, abbr, acronym, address, big, cite, code,
+
+del, dfn, em, img, ins, kbd, q, s, samp,
+
+small, strike, strong, sub, sup, tt, var,
+
+b, u, i, center,
+
+dl, dt, dd, ol, ul, li,
+
+fieldset, form, label, legend,
+
+table, caption, tbody, tfoot, thead, tr, th, td,
+
+article, aside, canvas, details, embed,
+
+figure, figcaption, footer, header, hgroup,
+
+menu, nav, output, ruby, section, summary,
+
+time, mark, audio, video {
+
+ margin: 0;
+
+ padding: 0;
+
+ border: 0;
+
+ font-size: 100%;
+
+ font: inherit;
+
+ vertical-align: baseline;
+
+}
+
+/* HTML5 display-role reset for older browsers */
+
+article, aside, details, figcaption, figure,
+
+footer, header, hgroup, menu, nav, section {
+
+ display: block;
+
+}
+
+body {
+
+ line-height: 1;
+
+}
+
+ol, ul {
+
+ list-style: none;
+
+}
+
+blockquote, q {
+
+ quotes: none;
+
+}
+
+blockquote:before, blockquote:after,
+
+q:before, q:after {
+
+ content: '';
+
+ content: none;
+
+}
+
+table {
+
+ border-collapse: collapse;
+
+ border-spacing: 0;
+
+}
\ No newline at end of file
--- /dev/null
+@import url(http://fonts.googleapis.com/css?family=Lato);
+@import url(http://fonts.googleapis.com/css?family=Oswald);
+
+/*****************
+HTML 5 Elements
+******************/
+new
+
+
+article, aside, details, figcaption, figure,
+footer, header, hgroup, menu, nav, section
+{
+ display: block;
+}
+
+
+.clearfix:after
+ {
+ visibility: hidden;
+ display: block;
+ font-size: 0;
+ content: " ";
+ clear: both;
+ height: 0;
+}
+
+
+/****************
+Body
+****************/
+
+body
+
+{
+ font: 76% arial,Helvetica,sans-serif;
+ text-align:left;
+ background:#fff;
+ color:#000;
+ border-top: 20px solid #555555;
+}
+
+
+
+/*********************
+Page Wrapper
+********************/
+
+#pageWrap
+
+{
+ width: 960px;
+ margin: 0 auto;
+ position:relative;
+}
+
+/**********************
+HEADER
+************************/
+
+#header
+{
+ display: block;
+ height: 180px;
+ margin: 0 auto 8px;
+ width: 960px;
+ position:relative;
+}
+
+#logo a
+{
+ background-image: url("../images/logo.jpg");
+ background-repeat: no-repeat;
+ height: 87px;
+ left: 0;
+ position: absolute;
+ top: 50px;
+ width: 361px;
+ margin-bottom:50px;
+}
+
+#buttons
+{
+height:88px;
+width:252px;
+float:right;
+ right: 0;
+ position: absolute;
+ top: 50px;
+}
+
+#buttons li
+{
+margin-bottom:10px;
+}
+
+#buttons #applet a
+{
+ background-image: url("../images/applet.jpg");
+ background-repeat: no-repeat;
+ height:50px;
+ width:250px;
+ position: absolute;
+ opacity: 1;
+ transition: opacity .25s ease-in-out;
+ -moz-transition: opacity .25s ease-in-out;
+ -webkit-transition: opacity .25s ease-in-out;
+ text-shadow: 2px 2px 10px #000000;
+}
+
+#buttons #desktop a
+{
+ background-image: url("../images/desk.jpg");
+ background-repeat: no-repeat;
+ height:50px;
+ width:250px;
+ position: absolute;
+ top:45px;
+ opacity: 1;
+ transition: opacity .25s ease-in-out;
+ -moz-transition: opacity .25s ease-in-out;
+ -webkit-transition: opacity .25s ease-in-out;
+ text-shadow: 2px 2px 10px #000000;
+}
+
+#buttons #applet a:hover
+{
+ opacity: 0.8;
+}
+
+#buttons #desktop a:hover
+{
+ opacity: 0.8;
+}
+
+/*****************************
+NAV
+*********************************/
+#nav
+{
+width:100%;
+max-width:100%;
+color:#fff;
+background:#555;
+height:80px;
+}
+
+#navInner
+{
+width:960px;
+margin:0 auto;
+position:relative;
+}
+
+
+#sddm
+{ margin: 0;
+ padding: 0;
+ z-index: 30;
+ position:relative;
+ top:27px;
+}
+
+#sddm li
+{ margin: 0;
+ padding:0;
+ list-style: none;
+ float: left;
+}
+
+#sddm li a
+{
+ color: #FFFFFF;
+ font-size: 13pt;
+ padding: 27px 15px 25px;
+ text-align: center;
+ text-decoration: none;
+ font-family: 'Lato',sans-serif;
+}
+
+#sddm li a.community:hover
+{
+background:#F78E1E;
+}
+
+#sddm li a.development:hover
+{
+background:#AEBF45;
+}
+
+#sddm li a.training:hover
+{
+background:#009DDC;
+}
+
+#sddm li a.download-right
+{
+float:right;
+position:relative;
+left:345px;
+display:block;
+clear:left;
+ margin-top: -27px;
+ padding: 27px 15px 25px;
+}
+
+
+ul#sddm li a:hover
+{
+ text-decoration: none;
+ background:#0083A9;
+}
+
+#sddm div
+{ position: absolute;
+ visibility: hidden;
+ margin: 0;
+ padding: 0;
+ background: #555;
+ border: 1px solid #000000;
+ top:50px;
+}
+
+ #sddm div a
+ { position: relative;
+ display: block;
+ margin: 0;
+ padding:8px;
+ width: 200px;
+ white-space: nowrap;
+ text-align: center;
+ text-decoration: none;
+ background: #555;
+ color: #fff;
+ border: 1px solid #000000;
+ background: #555;
+ }
+
+
+
+/*****************************
+CONTENT
+*****************************/
+
+#content
+{
+ font-size: 10pt;
+ height: auto;
+ width: 710px;
+ padding-top:23px;
+ padding-bottom:12px;
+ overflow-x:auto;
+ overflow-y:hidden;
+}
+#content h1
+{
+ padding-top:29px;
+ font-size: 15pt;
+ font-style: bold;
+}
+#content h2
+{
+ padding-top:27px;
+ font-size: 13pt;
+ font-style: bold;
+}
+#content h3
+{
+ padding-top:25px;
+ font-size: 12pt;
+ font-style: bold italic;
+}
+#content pre
+{
+ font-family: monospace;
+}
+#sideNav
+{
+width:200px;
+float:left;
+padding-top:29px;
+margin-right:50px;
+}
+#content ul
+{
+ list-style-type: disc;
+}
+#content li
+{
+ margin-left: 11px;
+ padding-bottom:11px;
+}
+
+#sideNav li
+{
+ height: 40px;
+ list-style-image: none;
+ list-style-type: none;
+ margin-bottom: 20px;
+}
+
+#sideNav a
+{
+ color: #555555;
+ display: block;
+ font-size: 13pt;
+ padding: 8px 0 0 15px;
+ text-decoration: none;
+}
+
+#sideNav a:hover
+{
+ text-decoration: underline;
+}
+#sideNav .about-nav-title
+{
+background: url("../images/normal-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .jvlite-nav-title
+{
+background: url("../images/jvlite-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .jvlite-nav-small
+{
+background: url("../images/jvlite-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 0px;
+}
+
+#sideNav .com-nav-title
+{
+background: url("../images/com-arrow-3-small.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .dev-nav-title
+{
+background: url("../images/dev-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#sideNav .train-nav-title
+{
+background: url("../images/train-arrow-3-normal.png") no-repeat scroll 0 0 transparent;
+ color: #FFFFFF;
+ font-family: 'Lato',sans-serif;
+ font-size: 18pt;
+ font-weight: normal;
+ height: 40px;
+ margin-bottom: 20px;
+ padding-left: 5px;
+}
+
+#content .borderTable td
+{
+ border: 1px solid black;
+}
+#content .borderTable tr
+{
+ border-bottom: 2px solid black;
+}
+
+td
+{
+ vertical-align: middle;
+}
+
+/********************************
+FOOTER
+***********************************/
+
+#footer
+{
+max-width:100%;
+width:100%;
+color:#fff;
+background:#555;
+height:140px;
+padding-top:10px;
+clear:both;
+}
+#innerFooter a
+{
+ color: #EEEEEE;
+ visited: #DDDDDD;
+
+}
+
+#innerFooter
+{
+width:960px;
+margin:0 auto;
+height:140px;
+padding-top:10px;
+}
+
+
+#copyright
+{
+float:left;
+}
+
+#cite
+{
+float:right;
+width:555px;
+}
\ No newline at end of file
--- /dev/null
+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+#
+# This file is part of Jalview.
+#
+# Jalview is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+#
+# Jalview is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+# PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+ST-TURN-IIL 705b23
+GAMMA-TURN-CLASSIC 788763
+BETA-TURN-IR 9a6a94
+BETA-TURN-IL d6a6ca
+BETA-BULGE 1dc451
+Pfam dc206a
+PHOSPHORYLATION (S) b974a5
+PHOSPHORYLATION (Y) 7d3881
+Cath 93b1d2
+ASX-TURN-IR 4ccc6e
+BETA-BULGE-LOOP-5 4066da
+CATMAT-4 4dc465
+CATMAT-3 3eb555
+GAMMA-TURN-INVERSE 7881c7
+SCHELLMANN-LOOP-6 a28bbb
+METAL cc9900
+ALPHA-BETA-MOTIF 7bd649
+ASX-MOTIF 6addbb
+NEST-LR 3e16d0
+ASX-TURN-IIR 6a4062
+NEST-RL 3e16b2
+ASX-TURN-IIL a67c98
+BETA-TURN-IIR c79792
+PHOSPHORYLATION (T) c88395
+BETA-TURN-IIL 8b5b50
+ST-MOTIF ac25a1
+
+STARTGROUP uniprot
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
+Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
+Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
+Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
+Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
+Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
+Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
+Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
+Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
+Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
+Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath
+ENDGROUP uniprot
+
+
+STARTGROUP netphos
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_CAPAA -1 89 89 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html> FER1_SOLLC -1 22 22 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER1_SOLLC -1 38 38 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 102_10</a></html> FER1_SOLLC -1 102 102 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html> FER1_SOLLC -1 136 136 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html> Q93XJ9_SOLTU -1 136 136 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html> Q93XJ9_SOLTU -1 22 22 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> Q93XJ9_SOLTU -1 38 38 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 33_3</a></html> FER1_PEA -1 33 33 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 42_4</a></html> FER1_PEA -1 42 42 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_PEA -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_PEA -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> FER1_PEA -1 4 4 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 28_2</a></html> FER1_PEA -1 28 28 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_PEA -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 117_11</a></html> Q7XA98_TRIPR -1 117 117 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 137_13</a></html> Q7XA98_TRIPR -1 137 137 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 144_14</a></html> Q7XA98_TRIPR -1 144 144 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 30_3</a></html> Q7XA98_TRIPR -1 30 30 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 31_3</a></html> Q7XA98_TRIPR -1 31 31 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> Q7XA98_TRIPR -1 4 4 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html> Q7XA98_TRIPR -1 45 45 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 46_4</a></html> Q7XA98_TRIPR -1 46 46 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 93_9</a></html> Q7XA98_TRIPR -1 93 93 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 88_8</a></html> FER1_SPIOL -1 88 88 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html> FER1_SPIOL -1 112 112 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html> FER1_SPIOL -1 139 139 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html> FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_ARATH -1 19 19 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> FER1_ARATH -1 24 24 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_ARATH -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> FER1_ARATH -1 75 75 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER_BRANA -1 38 38 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html> FER_BRANA -1 62 62 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_BRANA -1 89 89 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (Y) 23_2</a></html> FER_BRANA -1 23 23 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> Q93Z60_ARATH -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> Q93Z60_ARATH -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (T) 21_2</a></html> Q93Z60_ARATH -1 21 21 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> Q93Z60_ARATH -1 24 24 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> Q93Z60_ARATH -1 75 75 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 7_</a></html> FER1_MAIZE -1 7 7 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_MAIZE -1 19 19 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 44_4</a></html> FER1_MAIZE -1 44 44 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html> FER1_MAIZE -1 45 45 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_MAIZE -1 90 90 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_MAIZE -1 107 107 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_MAIZE -1 114 114 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (T) 134_13</a></html> FER1_MAIZE -1 134 134 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_MAIZE -1 141 141 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (Y) 115_11</a></html> FER1_MAIZE -1 115 115 PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (T) 133_13</a></html> O80429_MAIZE -1 133 133 PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 82_8</a></html> O80429_MAIZE -1 82 82 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 9_</a></html> O80429_MAIZE -1 9 9 PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 99_9</a></html> O80429_MAIZE -1 99 99 PHOSPHORYLATION (S)
+ENDGROUP netphos
+
+STARTGROUP s3dm
+<html>Found in PDBs: 1a70.,1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 115_11</a></html> FER1_SPIOL -1 115 119 ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturniil?gzip=false">ASX-TURN-IIL 107_10</a></html> FER1_SPIOL -1 107 109 ASX-TURN-IIL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturnir?gzip=false">ASX-TURN-IR 115_11</a></html> FER1_SPIOL -1 115 117 ASX-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betabulge?gzip=false">BETA-BULGE 102_10</a></html> FER1_SPIOL -1 102 103 BETA-BULGE
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 59_6</a></html> FER1_SPIOL -1 59 62 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 69_7</a></html> FER1_SPIOL -1 69 72 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 95_9</a></html> FER1_SPIOL -1 95 98 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 108_11</a></html> FER1_SPIOL -1 108 111 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 125_12</a></html> FER1_SPIOL -1 125 128 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 141_14</a></html> FER1_SPIOL -1 141 144 BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 90_9</a></html> FER1_SPIOL -1 90 92 NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html> FER1_SPIOL -1 92 94 NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 140_14</a></html> FER1_SPIOL -1 140 142 NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 81_8</a></html> FER1_SPIOL -1 81 83 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 89_9</a></html> FER1_SPIOL -1 89 91 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html> FER1_SPIOL -1 91 93 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 121_12</a></html> FER1_SPIOL -1 121 123 NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 78_8</a></html> FER1_SPIOL -1 78 83 SCHELLMANN-LOOP-6
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 118_12</a></html> FER1_SPIOL -1 118 123 SCHELLMANN-LOOP-6
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/stmotif?gzip=false">ST-MOTIF 59_6</a></html> FER1_SPIOL -1 59 63 ST-MOTIF
+ALPHA-BETA-MOTIF FER1_SPIOL -1 65 69 ALPHA-BETA-MOTIF
+ASX-MOTIF FER1_SPIOL -1 65 69 ASX-MOTIF
+ASX-TURN-IIL FER1_SPIOL -1 57 59 ASX-TURN-IIL
+ASX-TURN-IR FER1_SPIOL -1 65 67 ASX-TURN-IR
+BETA-BULGE FER1_SPIOL -1 52 53 BETA-BULGE
+BETA-TURN-IR FER1_SPIOL -1 9 12 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 19 22 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 45 48 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 58 61 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 75 78 BETA-TURN-IR
+BETA-TURN-IR FER1_SPIOL -1 91 94 BETA-TURN-IR
+NEST-LR FER1_SPIOL -1 40 42 NEST-LR
+NEST-LR FER1_SPIOL -1 42 44 NEST-LR
+NEST-LR FER1_SPIOL -1 90 92 NEST-LR
+NEST-RL FER1_SPIOL -1 31 33 NEST-RL
+NEST-RL FER1_SPIOL -1 39 41 NEST-RL
+NEST-RL FER1_SPIOL -1 41 43 NEST-RL
+NEST-RL FER1_SPIOL -1 71 73 NEST-RL
+SCHELLMANN-LOOP-6 FER1_SPIOL -1 28 33 SCHELLMANN-LOOP-6
+SCHELLMANN-LOOP-6 FER1_SPIOL -1 68 73 SCHELLMANN-LOOP-6
+ST-MOTIF FER1_SPIOL -1 9 13 ST-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 76_8</a></html> FER1_MAIZE -1 76 80 ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 77_8</a></html> FER1_MAIZE -1 77 81 ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 127_13</a></html> FER1_MAIZE -1 127 130 BETA-TURN-IR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturnclassic?gzip=false">GAMMA-TURN-CLASSIC 113_11</a></html> FER1_MAIZE -1 113 115 GAMMA-TURN-CLASSIC
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 59_6</a></html> FER1_MAIZE -1 59 61 GAMMA-TURN-INVERSE
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 104_10</a></html> FER1_MAIZE -1 104 106 GAMMA-TURN-INVERSE
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html> FER1_MAIZE -1 92 94 NEST-LR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 94_9</a></html> FER1_MAIZE -1 94 96 NEST-LR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 83_8</a></html> FER1_MAIZE -1 83 85 NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html> FER1_MAIZE -1 91 93 NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 93_9</a></html> FER1_MAIZE -1 93 95 NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 123_12</a></html> FER1_MAIZE -1 123 125 NEST-RL
+ALPHA-BETA-MOTIF FER1_MAIZE -1 132 136 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 174 178 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 175 179 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 180 184 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 181 185 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 214 218 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 215 219 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 218 222 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 223 227 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 246 250 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 251 255 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 254 258 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 258 262 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 279 283 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 280 284 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 289 293 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 296 300 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 299 303 ALPHA-BETA-MOTIF
+ASX-TURN-IIL FER1_MAIZE -1 160 162 ASX-TURN-IIL
+ASX-TURN-IIR FER1_MAIZE -1 107 109 ASX-TURN-IIR
+BETA-BULGE FER1_MAIZE -1 31 32 BETA-BULGE
+BETA-BULGE FER1_MAIZE -1 43 44 BETA-BULGE
+BETA-TURN-IIL FER1_MAIZE -1 170 173 BETA-TURN-IIL
+BETA-TURN-IIR FER1_MAIZE -1 71 74 BETA-TURN-IIR
+BETA-TURN-IIR FER1_MAIZE -1 140 143 BETA-TURN-IIR
+BETA-TURN-IIR FER1_MAIZE -1 274 277 BETA-TURN-IIR
+BETA-TURN-IL FER1_MAIZE -1 64 67 BETA-TURN-IL
+BETA-TURN-IR FER1_MAIZE -1 33 36 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 50 53 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 100 103 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 103 106 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 136 139 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 171 174 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 172 175 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 206 209 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 207 210 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 223 226 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 233 236 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 252 255 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 264 267 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 289 292 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 295 298 BETA-TURN-IR
+CATMAT-3 FER1_MAIZE -1 20 22 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 47 49 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 97 99 CATMAT-3
+CATMAT-4 FER1_MAIZE -1 189 192 CATMAT-4
+GAMMA-TURN-INVERSE FER1_MAIZE -1 68 70 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 84 86 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 232 234 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 240 242 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 244 246 GAMMA-TURN-INVERSE
+NEST-LR FER1_MAIZE -1 30 32 NEST-LR
+NEST-LR FER1_MAIZE -1 66 68 NEST-LR
+NEST-LR FER1_MAIZE -1 106 108 NEST-LR
+NEST-LR FER1_MAIZE -1 108 110 NEST-LR
+NEST-LR FER1_MAIZE -1 212 214 NEST-LR
+NEST-LR FER1_MAIZE -1 276 278 NEST-LR
+NEST-LR FER1_MAIZE -1 307 309 NEST-LR
+NEST-RL FER1_MAIZE -1 64 66 NEST-RL
+NEST-RL FER1_MAIZE -1 105 107 NEST-RL
+NEST-RL FER1_MAIZE -1 107 109 NEST-RL
+NEST-RL FER1_MAIZE -1 306 308 NEST-RL
+ST-TURN-IIL FER1_MAIZE -1 20 22 ST-TURN-IIL
+ALPHA-BETA-MOTIF FER1_MAIZE -1 24 28 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 25 29 ALPHA-BETA-MOTIF
+BETA-TURN-IR FER1_MAIZE -1 75 78 BETA-TURN-IR
+GAMMA-TURN-CLASSIC FER1_MAIZE -1 61 63 GAMMA-TURN-CLASSIC
+GAMMA-TURN-INVERSE FER1_MAIZE -1 7 9 GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE FER1_MAIZE -1 52 54 GAMMA-TURN-INVERSE
+NEST-LR FER1_MAIZE -1 40 42 NEST-LR
+NEST-LR FER1_MAIZE -1 42 44 NEST-LR
+NEST-RL FER1_MAIZE -1 31 33 NEST-RL
+NEST-RL FER1_MAIZE -1 39 41 NEST-RL
+NEST-RL FER1_MAIZE -1 41 43 NEST-RL
+NEST-RL FER1_MAIZE -1 71 73 NEST-RL
+ALPHA-BETA-MOTIF FER1_MAIZE -1 176 180 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 233 237 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 247 251 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 278 282 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 286 290 ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF FER1_MAIZE -1 295 299 ALPHA-BETA-MOTIF
+ASX-MOTIF FER1_MAIZE -1 122 126 ASX-MOTIF
+ASX-MOTIF FER1_MAIZE -1 160 164 ASX-MOTIF
+ASX-TURN-IR FER1_MAIZE -1 122 124 ASX-TURN-IR
+BETA-BULGE-LOOP-5 FER1_MAIZE -1 122 126 BETA-BULGE-LOOP-5
+BETA-BULGE-LOOP-5 FER1_MAIZE -1 239 243 BETA-BULGE-LOOP-5
+BETA-TURN-IR FER1_MAIZE -1 122 125 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 160 163 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 239 242 BETA-TURN-IR
+BETA-TURN-IR FER1_MAIZE -1 261 264 BETA-TURN-IR
+CATMAT-3 FER1_MAIZE -1 80 82 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 87 89 CATMAT-3
+CATMAT-3 FER1_MAIZE -1 262 264 CATMAT-3
+NEST-RL FER1_MAIZE -1 124 126 NEST-RL
+NEST-RL FER1_MAIZE -1 241 243 NEST-RL
+NEST-RL FER1_MAIZE -1 292 294 NEST-RL
+ENDGROUP s3dm
--- /dev/null
+(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);\r
--- /dev/null
+/*********\r
+ * downloaded from http://java.com/js/deployJava.js\r
+ * Probably copyright Oracle nee Sun 2011,2010,2009.\r
+ */\r
+var deployJava={debug:null,firefoxJavaVersion:null,myInterval:null,preInstallJREList:null,returnPage:null,brand:null,locale:null,installType:null,EAInstallEnabled:false,EarlyAccessURL:null,getJavaURL:'http://java.sun.com/webapps/getjava/BrowserRedirect?host=java.com',appleRedirectPage:'http://www.apple.com/support/downloads/',oldMimeType:'application/npruntime-scriptable-plugin;DeploymentToolkit',mimeType:'application/java-deployment-toolkit',launchButtonPNG:'http://java.sun.com/products/jfc/tsc/articles/swing2d/webstart.png',browserName:null,browserName2:null,getJREs:function(){var list=new Array();if(deployJava.isPluginInstalled()){var plugin=deployJava.getPlugin();var VMs=plugin.jvms;for(var i=0;i<VMs.getLength();i++){list[i]=VMs.get(i).version;}}else{var browser=deployJava.getBrowser();if(browser=='MSIE'){if(deployJava.testUsingActiveX('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingActiveX('1.6.0')){list[0]='1.6.0';}else if(deployJava.testUsingActiveX('1.5.0')){list[0]='1.5.0';}else if(deployJava.testUsingActiveX('1.4.2')){list[0]='1.4.2';}else if(deployJava.testForMSVM()){list[0]='1.1';}}else if(browser=='Netscape Family'){deployJava.getJPIVersionUsingMimeType();if(deployJava.firefoxJavaVersion!=null){list[0]=deployJava.firefoxJavaVersion;}else if(deployJava.testUsingMimeTypes('1.7')){list[0]='1.7.0';}else if(deployJava.testUsingMimeTypes('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingMimeTypes('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingMimeTypes('1.4.2')){list[0]='1.4.2';}else if(deployJava.browserName2=='Safari'){if(deployJava.testUsingPluginsArray('1.7.0')){list[0]='1.7.0';}else if(deployJava.testUsingPluginsArray('1.6')){list[0]='1.6.0';}else if(deployJava.testUsingPluginsArray('1.5')){list[0]='1.5.0';}else if(deployJava.testUsingPluginsArray('1.4.2')){list[0]='1.4.2';}}}}\r
+if(deployJava.debug){for(var i=0;i<list.length;++i){alert('We claim to have detected Java SE '+list[i]);}}\r
+return list;},installJRE:function(requestVersion){var ret=false;if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installJRE(requestVersion)){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
+return true;}else{return false;}}else{return deployJava.installLatestJRE();}},installLatestJRE:function(){if(deployJava.isPluginInstalled()){if(deployJava.getPlugin().installLatestJRE()){deployJava.refresh();if(deployJava.returnPage!=null){document.location=deployJava.returnPage;}\r
+return true;}else{return false;}}else{var browser=deployJava.getBrowser();var platform=navigator.platform.toLowerCase();if((deployJava.EAInstallEnabled=='true')&&(platform.indexOf('win')!=-1)&&(deployJava.EarlyAccessURL!=null)){deployJava.preInstallJREList=deployJava.getJREs();if(deployJava.returnPage!=null){deployJava.myInterval=setInterval("deployJava.poll()",3000);}\r
+location.href=deployJava.EarlyAccessURL;return false;}else{if(browser=='MSIE'){return deployJava.IEInstall();}else if((browser=='Netscape Family')&&(platform.indexOf('win32')!=-1)){return deployJava.FFInstall();}else{location.href=deployJava.getJavaURL+\r
+((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
+((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
+((deployJava.brand!=null)?('&brand='+deployJava.brand):'');}\r
+return false;}}},runApplet:function(attributes,parameters,minimumVersion){if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.1';}\r
+var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(deployJava.returnPage==null){deployJava.returnPage=document.location;}\r
+if(matchData!=null){var browser=deployJava.getBrowser();if((browser!='?')&&('Safari'!=deployJava.browserName2)){if(deployJava.versionCheck(minimumVersion+'+')){deployJava.writeAppletTag(attributes,parameters);}else if(deployJava.installJRE(minimumVersion+'+')){deployJava.refresh();location.href=document.location;deployJava.writeAppletTag(attributes,parameters);}}else{deployJava.writeAppletTag(attributes,parameters);}}else{if(deployJava.debug){alert('Invalid minimumVersion argument to runApplet():'+\r
+minimumVersion);}}},writeAppletTag:function(attributes,parameters){var startApplet='<'+'applet ';var params='';var endApplet='<'+'/'+'applet'+'>';var addCodeAttribute=true;for(var attribute in attributes){startApplet+=(' '+attribute+'="'+attributes[attribute]+'"');if(attribute=='code'||attribute=='java_code'){addCodeAttribute=false;}}\r
+if(parameters!='undefined'&¶meters!=null){var codebaseParam=false;for(var parameter in parameters){if(parameter=='codebase_lookup'){codebaseParam=true;}\r
+if(parameter=='object'||parameter=='java_object'){addCodeAttribute=false;}\r
+params+='<param name="'+parameter+'" value="'+\r
+parameters[parameter]+'"/>';}\r
+if(!codebaseParam){params+='<param name="codebase_lookup" value="false"/>';}}\r
+if(addCodeAttribute){startApplet+=(' code="dummy"');}\r
+startApplet+='>';document.write(startApplet+'\n'+params+'\n'+endApplet);},versionCheck:function(versionPattern)\r
+{var index=0;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?(\\*|\\+)?$";var matchData=versionPattern.match(regex);if(matchData!=null){var familyMatch=true;var patternArray=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!='')){patternArray[index]=matchData[i];index++;}}\r
+if(patternArray[patternArray.length-1]=='+'){familyMatch=false;patternArray.length--;}else{if(patternArray[patternArray.length-1]=='*'){patternArray.length--;}}\r
+var list=deployJava.getJREs();for(var i=0;i<list.length;++i){if(deployJava.compareVersionToPattern(list[i],patternArray,familyMatch)){return true;}}\r
+return false;}else{alert('Invalid versionPattern passed to versionCheck: '+\r
+versionPattern);return false;}},isWebStartInstalled:function(minimumVersion){var browser=deployJava.getBrowser();if((browser=='?')||('Safari'==deployJava.browserName2)){return true;}\r
+if(minimumVersion=='undefined'||minimumVersion==null){minimumVersion='1.4.2';}\r
+var retval=false;var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=minimumVersion.match(regex);if(matchData!=null){retval=deployJava.versionCheck(minimumVersion+'+');}else{if(deployJava.debug){alert('Invalid minimumVersion argument to isWebStartInstalled(): '+minimumVersion);}\r
+retval=deployJava.versionCheck('1.4.2+');}\r
+return retval;},getJPIVersionUsingMimeType:function(){for(var i=0;i<navigator.mimeTypes.length;++i){var s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet;jpi-version=(.*)$/);if(m!=null){deployJava.firefoxJavaVersion=m[1];if('Opera'!=deployJava.browserName2){break;}}}},launchWebStartApplication:function(jnlp){var uaString=navigator.userAgent.toLowerCase();deployJava.getJPIVersionUsingMimeType();if(deployJava.isWebStartInstalled('1.7.0')==false){if((deployJava.installJRE('1.7.0+')==false)||((deployJava.isWebStartInstalled('1.7.0')==false))){return false;}}\r
+var jnlpDocbase=null;if(document.documentURI){jnlpDocbase=document.documentURI;}\r
+if(jnlpDocbase==null){jnlpDocbase=document.URL;}\r
+var browser=deployJava.getBrowser();var launchTag;if(browser=='MSIE'){launchTag='<'+'object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" '+'width="0" height="0">'+'<'+'PARAM name="launchjnlp" value="'+jnlp+'"'+'>'+'<'+'PARAM name="docbase" value="'+jnlpDocbase+'"'+'>'+'<'+'/'+'object'+'>';}else if(browser=='Netscape Family'){launchTag='<'+'embed type="application/x-java-applet;jpi-version='+\r
+deployJava.firefoxJavaVersion+'" '+'width="0" height="0" '+'launchjnlp="'+jnlp+'"'+'docbase="'+jnlpDocbase+'"'+' />';}\r
+if(document.body=='undefined'||document.body==null){document.write(launchTag);document.location=jnlpDocbase;}else{var divTag=document.createElement("div");divTag.id="div1";divTag.style.position="relative";divTag.style.left="-10000px";divTag.style.margin="0px auto";divTag.className="dynamicDiv";divTag.innerHTML=launchTag;document.body.appendChild(divTag);}},createWebStartLaunchButtonEx:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
+var url='javascript:deployJava.launchWebStartApplication(\''+jnlp+'\');';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},createWebStartLaunchButton:function(jnlp,minimumVersion){if(deployJava.returnPage==null){deployJava.returnPage=jnlp;}\r
+var url='javascript:'+'if (!deployJava.isWebStartInstalled("'+\r
+minimumVersion+'")) {'+'if (deployJava.installLatestJRE()) {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}'+'} else {'+'if (deployJava.launch("'+jnlp+'")) {}'+'}';document.write('<'+'a href="'+url+'" onMouseOver="window.status=\'\'; '+'return true;"><'+'img '+'src="'+deployJava.launchButtonPNG+'" '+'border="0" /><'+'/'+'a'+'>');},launch:function(jnlp){document.location=jnlp;return true;},isPluginInstalled:function(){var plugin=deployJava.getPlugin();if(plugin&&plugin.jvms){return true;}else{return false;}},isAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().isAutoUpdateEnabled();}\r
+return false;},setAutoUpdateEnabled:function(){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAutoUpdateEnabled();}\r
+return false;},setInstallerType:function(type){deployJava.installType=type;if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setInstallerType(type);}\r
+return false;},setAdditionalPackages:function(packageList){if(deployJava.isPluginInstalled()){return deployJava.getPlugin().setAdditionalPackages(packageList);}\r
+return false;},setEarlyAccess:function(enabled){deployJava.EAInstallEnabled=enabled;},isPlugin2:function(){if(deployJava.isPluginInstalled()){if(deployJava.versionCheck('1.6.0_10+')){try{return deployJava.getPlugin().isPlugin2();}catch(err){}}}\r
+return false;},allowPlugin:function(){deployJava.getBrowser();var ret=('Safari'!=deployJava.browserName2&&'Opera'!=deployJava.browserName2);return ret;},getPlugin:function(){deployJava.refresh();var ret=null;if(deployJava.allowPlugin()){ret=document.getElementById('deployJavaPlugin');}\r
+return ret;},compareVersionToPattern:function(version,patternArray,familyMatch){var regex="^(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(?:_(\\d+))?)?)?$";var matchData=version.match(regex);if(matchData!=null){var index=0;var result=new Array();for(var i=1;i<matchData.length;++i){if((typeof matchData[i]=='string')&&(matchData[i]!=''))\r
+{result[index]=matchData[i];index++;}}\r
+var l=Math.min(result.length,patternArray.length);if(familyMatch){for(var i=0;i<l;++i){if(result[i]!=patternArray[i])return false;}\r
+return true;}else{for(var i=0;i<l;++i){if(result[i]<patternArray[i]){return false;}else if(result[i]>patternArray[i]){return true;}}\r
+return true;}}else{return false;}},getBrowser:function(){if(deployJava.browserName==null){var browser=navigator.userAgent.toLowerCase();if(deployJava.debug){alert('userAgent -> '+browser);}\r
+if(browser.indexOf('msie')!=-1){deployJava.browserName='MSIE';deployJava.browserName2='MSIE';}else if(browser.indexOf('iphone')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='iPhone';}else if(browser.indexOf('firefox')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Firefox';}else if(browser.indexOf('chrome')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Chrome';}else if(browser.indexOf('safari')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Safari';}else if(browser.indexOf('mozilla')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Other';}else if(browser.indexOf('opera')!=-1){deployJava.browserName='Netscape Family';deployJava.browserName2='Opera';}else{deployJava.browserName='?';deployJava.browserName2='unknown';}\r
+if(deployJava.debug){alert('Detected browser name:'+deployJava.browserName+', '+deployJava.browserName2);}}\r
+return deployJava.browserName;},testUsingActiveX:function(version){var objectName='JavaWebStart.isInstalled.'+version+'.0';if(!ActiveXObject){if(deployJava.debug){alert('Browser claims to be IE, but no ActiveXObject object?');}\r
+return false;}\r
+try{return(new ActiveXObject(objectName)!=null);}catch(exception){return false;}},testForMSVM:function(){var clsid='{08B0E5C0-4FCB-11CF-AAA5-00401C608500}';if(typeof oClientCaps!='undefined'){var v=oClientCaps.getComponentVersion(clsid,"ComponentID");if((v=='')||(v=='5,0,5000,0')){return false;}else{return true;}}else{return false;}},testUsingMimeTypes:function(version){if(!navigator.mimeTypes){if(deployJava.debug){alert('Browser claims to be Netscape family, but no mimeTypes[] array?');}\r
+return false;}\r
+for(var i=0;i<navigator.mimeTypes.length;++i){s=navigator.mimeTypes[i].type;var m=s.match(/^application\/x-java-applet\x3Bversion=(1\.8|1\.7|1\.6|1\.5|1\.4\.2)$/);if(m!=null){if(deployJava.compareVersions(m[1],version)){return true;}}}\r
+return false;},testUsingPluginsArray:function(version){if((!navigator.plugins)||(!navigator.plugins.length)){return false;}\r
+var platform=navigator.platform.toLowerCase();for(var i=0;i<navigator.plugins.length;++i){s=navigator.plugins[i].description;if(s.search(/^Java Switchable Plug-in (Cocoa)/)!=-1){if(deployJava.compareVersions("1.5.0",version)){return true;}}else if(s.search(/^Java/)!=-1){if(platform.indexOf('win')!=-1){if(deployJava.compareVersions("1.5.0",version)||deployJava.compareVersions("1.6.0",version)){return true;}}}}\r
+if(deployJava.compareVersions("1.5.0",version)){return true;}\r
+return false;},IEInstall:function(){location.href=deployJava.getJavaURL+\r
+((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
+((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
+((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
+((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},done:function(name,result){},FFInstall:function(){location.href=deployJava.getJavaURL+\r
+((deployJava.returnPage!=null)?('&returnPage='+deployJava.returnPage):'')+\r
+((deployJava.locale!=null)?('&locale='+deployJava.locale):'')+\r
+((deployJava.brand!=null)?('&brand='+deployJava.brand):'')+\r
+((deployJava.installType!=null)?('&type='+deployJava.installType):'');return false;},compareVersions:function(installed,required){var a=installed.split('.');var b=required.split('.');for(var i=0;i<a.length;++i){a[i]=Number(a[i]);}\r
+for(var i=0;i<b.length;++i){b[i]=Number(b[i]);}\r
+if(a.length==2){a[2]=0;}\r
+if(a[0]>b[0])return true;if(a[0]<b[0])return false;if(a[1]>b[1])return true;if(a[1]<b[1])return false;if(a[2]>b[2])return true;if(a[2]<b[2])return false;return true;},enableAlerts:function(){deployJava.browserName=null;deployJava.debug=true;},poll:function(){deployJava.refresh();var postInstallJREList=deployJava.getJREs();if((deployJava.preInstallJREList.length==0)&&(postInstallJREList.length!=0)){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;};}\r
+if((deployJava.preInstallJREList.length!=0)&&(postInstallJREList.length!=0)&&(deployJava.preInstallJREList[0]!=postInstallJREList[0])){clearInterval(deployJava.myInterval);if(deployJava.returnPage!=null){location.href=deployJava.returnPage;}}},writePluginTag:function(){var browser=deployJava.getBrowser();if(browser=='MSIE'){document.write('<'+'object classid="clsid:CAFEEFAC-DEC7-0000-0000-ABCDEFFEDCBA" '+'id="deployJavaPlugin" width="0" height="0">'+'<'+'/'+'object'+'>');}else if(browser=='Netscape Family'&&deployJava.allowPlugin()){deployJava.writeEmbedTag();}},refresh:function(){navigator.plugins.refresh(false);var browser=deployJava.getBrowser();if(browser=='Netscape Family'&&deployJava.allowPlugin()){var plugin=document.getElementById('deployJavaPlugin');if(plugin==null){deployJava.writeEmbedTag();}}},writeEmbedTag:function(){var written=false;if(navigator.mimeTypes!=null){for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.mimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
+deployJava.mimeType+'" hidden="true" />');written=true;}}}\r
+if(!written)for(var i=0;i<navigator.mimeTypes.length;i++){if(navigator.mimeTypes[i].type==deployJava.oldMimeType){if(navigator.mimeTypes[i].enabledPlugin){document.write('<'+'embed id="deployJavaPlugin" type="'+\r
+deployJava.oldMimeType+'" hidden="true" />');}}}}},do_initialize:function(){deployJava.writePluginTag();if(deployJava.locale==null){var loc=null;if(loc==null)try{loc=navigator.userLanguage;}catch(err){}\r
+if(loc==null)try{loc=navigator.systemLanguage;}catch(err){}\r
+if(loc==null)try{loc=navigator.language;}catch(err){}\r
+if(loc!=null){loc.replace("-","_")\r
+deployJava.locale=loc;}}}};deployJava.do_initialize();
\ No newline at end of file
--- /dev/null
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+// default console to report messages
+var _console = document.getElementById("stdout");
+var _jvapps = new Array();
+// jvjmols is a list associating a jmol id to { modelstofiles }
+var _jvjmols = new Hashtable();
+// array of model names used to lookup index in Jmol
+var _modeltofiles = new Array();
+// counter for jmol structures
+var mnum = 1;
+
+function setConsole(console) {
+ _console = console;
+}
+
+function getDestinationFrms(source, frames) {
+ var frms = new Array();
+ var frid = "";
+ for (frm in frames) {
+ try {
+ frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
+ .getSequenceSetId()));
+ } catch (q) {
+ };
+
+ if (!frames[frm].equals(source) && !frid
+ && !frames[frm].currentAlignFrame.equals(source)) {
+ frms[frms.length] = frames[frm];
+ }
+ }
+ return frms;
+}
+
+function mouseover(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
+ + list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
+
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].highlight(list[1], list[2], "true");
+ }
+ return true;
+}
+
+function sellist(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
+ + list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
+ list[2], list[3])
+ }
+ return true;
+}
+
+function viewlist(list1, list2, list3, list4) {
+ // list1 = new Object(list1);
+ var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+ var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
+ + " id : " + list[1] + "\nRow from " + list[2] + " and to "
+ + list[3] + "\nVisible columns: " + list[4] + "\n";
+ var flist = getDestinationFrms(list1, _jvapps);
+ if (_console) {
+ _console.value = msg + "\n";
+ }
+
+ for (follower in flist) {
+ if (_console) {
+ _console.value += "Sending to " + flist[follower] + "\n";
+ }
+ flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
+ list[2], "-1");
+ }
+ return true;
+}
+
+// register a jalview applet and add some handlers to it
+// jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
+function linkJvJmol(applet, jmolView, modeltofiles) {
+ var i = _jvapps.length;
+ while (i--) {
+ if (_jvapps[i].equals(applet)) {
+ throw ("Ignoring additional linkJvJmol call for "
+ + applet.getName() + ".");
+ }
+ }
+ _jvapps[_jvapps.length] = applet;
+ applet.setMouseoverListener("mouseover");
+ applet.setSelectionListener("sellist");
+ // viewListener not fully implemented in 2.7
+ // try { applet.setViewListener("viewlist"); } catch (err) {};
+ if (jmolView)
+ {
+ var sep = applet.getSeparator();
+ var oldjm=jmolView;
+ // recover full id of Jmol applet
+ jmolView=_jmolGetApplet(jmolView).id;
+ var jmbinding=_jvjmols.get(jmolView);
+ if (!jmbinding)
+ {
+ jmbinding=new Object();
+ jmbinding._modelstofiles=new Array();
+ jmbinding._fullmpath=new Array();
+ jmbinding._filetonum=new Hashtable();
+ jmbinding._jmol=jmolView;
+ jmbinding._jmhandle=oldjm;
+ _jvjmols.put(jmolView,jmbinding);
+ }
+
+ jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
+ jmbinding._jmol=jmolView;
+ // now update structureListener list
+ mtf="";
+ var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
+ for (m in jmbinding._modelstofiles)
+ { if (m>0) { mtf+=sep; }
+ mtf+=jmbinding._modelstofiles[m];
+ if (jmbinding._modelstofiles[m].indexOf("//")==-1)
+ { jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
+ jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1);
+ jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
+
+ }
+ applet.setStructureListener("_structure", mtf);
+ }
+}
+
+/*function _addJmolModel(jmolid, modelname) {
+ modelname=""+modelname;
+ var jminf = _jvjmols[jmolid];
+ if (!jminf) {
+ jminf = new Object();
+ jminf._modelstofiles = new Array(); //new Hashtable();
+ jminf._jmol = jmolid;
+ jminf._modellist=new Array();
+ _jvjmols[jmolid] = jminf;
+ }
+ var obj = new Object();
+ jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
+ obj.id = modelname;
+ obj.mnum = jminf._modeltofiles.length;
+ jminf._modellist+=modelname;
+}*/
+
+
+
+// jmol Jalview Methods
+
+function _structure(list1, list2, list3, list4) {
+ var follower;
+ // if (_console) { if (!_console.value) { _console.value="";} }
+ if (list1 == "mouseover") {
+ var list = new Array(("" + list1), ("" + list2), ("" + list3),
+ ("" + list4));
+ // 1 is pdb file, 2 is residue number, 3 is chain
+ // list1 = new Object(list1);
+ var base = list[1].indexOf(document.baseURI
+ .substring(0, document.baseURI.lastIndexOf('/'))
+ ); // .indexOf(_path);
+ if (base==0) { base = document.baseURI.lastIndexOf('/'); }
+ var sid = list[1]; // .substring(base);
+ base = list[1].substring(0, base);
+ if (_console) {
+ _console.value += "Model is " + list[1] + ", Structure id is : "
+ + sid + "\n";
+ }
+ ;
+ var siddat;
+ for ( var jmolappi in _jvjmols.values()) {
+ var jmolapp=_jvjmols.values()[jmolappi];
+ var msg = "";
+ if (siddat = jmolapp._filetonum.get(sid)) {
+ // we don't putin chain number because there isn't one ?
+ // skip select 0 bit
+ var ch = ""+list[3];
+ if ((""+list[2]).trim().length==1)
+ {
+ ch+=":"+list[2];
+ }
+ msg = "select (" + ch + " /" + siddat + ") ;";
+ }
+ if (msg) {
+ if (_console) {
+ _console.value += "Sending '" + msg + "' to jmol." + "\n";
+ }
+ }
+ jmolScriptWait(msg, "" + jmolapp._jmhandle);
+ // only do highlight for one jmol ?
+ // return 1;
+ }
+ }
+ if (list1 == "colourstruct") {
+ if (_console) {
+ _console.value += 'colourStruct("' + list1 + '","' + list2
+ + '") [' + list4 + ']' + "\n";
+ }
+ setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
+ return 1;
+ }
+ return 1;
+}
+// last colour message
+var _lastMsg = "";
+// indicator - if _colourStruct==0 then no colouring is going on
+var _colourStruct = 0;
+
+function colourStruct(involves, msg, handle) {
+ if (_colourStruct == 0) {
+ _colourStruct = 1;
+ for (ap in _jvapps) {
+ var _msg = "";
+ do {
+ if (_msg.match(/\S/)) {
+ _lastMsg += _msg;
+ }
+ _msg = "" + _jvapps[ap].getJsMessage(msg, handle);
+ } while (_msg.match(/\S/));
+ }
+ // locate the jmol that should get the message
+ for (var jmol in _jvjmols.values())
+ {
+ var jml=_jvjmols.values()[jmol];
+ if (jml._filetonum.get(involves))
+ {
+ colourStructs(jml._jmhandle);
+ }
+ }
+ _colourStruct = 0;
+ } else {
+ // setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
+ }
+}
+
+function colourStructs(jmolapp) {
+ dbg(0, "Colouring the structures\n");
+ jmolScriptWait("set selectionhalos false;" + _lastMsg
+ + "; select 0; set selectionhalos true;", jmolapp);
+ _lastMsg = "";
+}
+var _jmolhovermsg="";
+function _jmolhover(jmid, atomlabel, atomidx) {
+ var msg=""+jmid+" "+atomlabel+" "+atomidx;
+ if (_jmolhovermsg==msg)
+ {
+ return;
+ }
+ _jmolhovermsg=msg;
+ modeltofiles = _jvjmols.get(jmid)._modelstofiles;
+ // atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
+ // relaxed third parameter - may be null or a model number for multi model
+ // views
+ atomlabel = ("" + atomlabel)
+ .match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
+ atomidx = "" + atomidx;
+ if (atomlabel[5]) {
+ atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
+ atomlabel[5] = parseInt(atomlabel[5])-1;
+ } else {
+ // default - first model
+ atomlabel[5] = 0;
+ }
+ // use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
+ for (ap in _jvapps) {
+ _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
+ document.baseURI
+ .substring(0, document.baseURI.lastIndexOf('/'))
+ + "/" +
+ modeltofiles[atomlabel[5]]);
+ msg = _jmolhovermsg;
+ }
+}
+function _jmolpick(jmid, atomlabel, atomidx) {
+ atomlabel = "" + atomlabel;
+ atomidx = "" + atomidx;
+ // label is atom id, atom number, and xyz coordinates in the form:
+ // C6 #6 -0.30683374 -1.6836332 -0.716934
+ // atom index, starting with 0.
+
+}
+function _jmolMessagecallback(jmid, statmess) {
+ // if (statmess.indexOf("Script Terminated")==0)
+ {
+ var thisTime = new Date();
+ if (_console) {
+ _console.value += "Last script execution took : "
+ + (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
+ + " seconds.";
+ }
+ _lastTime = thisTime;
+
+ }
+}
--- /dev/null
+/*!
+ * jQuery JavaScript Library v1.4.4
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Thu Nov 11 19:04:53 2010 -0500
+ */
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+3),a,b,d);else{d=0;for(var e=this.length;d<e;d++){a=this[d];b=a.style.display;if(!c.data(a,"olddisplay")&&b==="none")b=a.style.display="";b===""&&c.css(a,"display")==="none"&&c.data(a,"olddisplay",qa(a.nodeName))}for(d=0;d<e;d++){a=this[d];b=a.style.display;if(b===""||b==="none")a.style.display=c.data(a,"olddisplay")||""}return this}},hide:function(a,b,d){if(a||a===0)return this.animate(S("hide",3),a,b,d);else{a=0;for(b=this.length;a<b;a++){d=c.css(this[a],"display");d!=="none"&&c.data(this[a],"olddisplay",
+d)}for(a=0;a<b;a++)this[a].style.display="none";return this}},_toggle:c.fn.toggle,toggle:function(a,b,d){var e=typeof a==="boolean";if(c.isFunction(a)&&c.isFunction(b))this._toggle.apply(this,arguments);else a==null||e?this.each(function(){var f=e?a:c(this).is(":hidden");c(this)[f?"show":"hide"]()}):this.animate(S("toggle",3),a,b,d);return this},fadeTo:function(a,b,d,e){return this.filter(":hidden").css("opacity",0).show().end().animate({opacity:b},a,d,e)},animate:function(a,b,d,e){var f=c.speed(b,
+d,e);if(c.isEmptyObject(a))return this.each(f.complete);return this[f.queue===false?"each":"queue"](function(){var h=c.extend({},f),l,k=this.nodeType===1,o=k&&c(this).is(":hidden"),x=this;for(l in a){var r=c.camelCase(l);if(l!==r){a[r]=a[l];delete a[l];l=r}if(a[l]==="hide"&&o||a[l]==="show"&&!o)return h.complete.call(this);if(k&&(l==="height"||l==="width")){h.overflow=[this.style.overflow,this.style.overflowX,this.style.overflowY];if(c.css(this,"display")==="inline"&&c.css(this,"float")==="none")if(c.support.inlineBlockNeedsLayout)if(qa(this.nodeName)===
+"inline")this.style.display="inline-block";else{this.style.display="inline";this.style.zoom=1}else this.style.display="inline-block"}if(c.isArray(a[l])){(h.specialEasing=h.specialEasing||{})[l]=a[l][1];a[l]=a[l][0]}}if(h.overflow!=null)this.style.overflow="hidden";h.curAnim=c.extend({},a);c.each(a,function(A,C){var J=new c.fx(x,h,A);if(vb.test(C))J[C==="toggle"?o?"show":"hide":C](a);else{var w=wb.exec(C),I=J.cur()||0;if(w){var L=parseFloat(w[2]),g=w[3]||"px";if(g!=="px"){c.style(x,A,(L||1)+g);I=(L||
+1)/J.cur()*I;c.style(x,A,I+g)}if(w[1])L=(w[1]==="-="?-1:1)*L+I;J.custom(I,L,g)}else J.custom(I,C,"")}});return true})},stop:function(a,b){var d=c.timers;a&&this.queue([]);this.each(function(){for(var e=d.length-1;e>=0;e--)if(d[e].elem===this){b&&d[e](true);d.splice(e,1)}});b||this.dequeue();return this}});c.each({slideDown:S("show",1),slideUp:S("hide",1),slideToggle:S("toggle",1),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(a,b){c.fn[a]=function(d,e,f){return this.animate(b,
+d,e,f)}});c.extend({speed:function(a,b,d){var e=a&&typeof a==="object"?c.extend({},a):{complete:d||!d&&b||c.isFunction(a)&&a,duration:a,easing:d&&b||b&&!c.isFunction(b)&&b};e.duration=c.fx.off?0:typeof e.duration==="number"?e.duration:e.duration in c.fx.speeds?c.fx.speeds[e.duration]:c.fx.speeds._default;e.old=e.complete;e.complete=function(){e.queue!==false&&c(this).dequeue();c.isFunction(e.old)&&e.old.call(this)};return e},easing:{linear:function(a,b,d,e){return d+e*a},swing:function(a,b,d,e){return(-Math.cos(a*
+Math.PI)/2+0.5)*e+d}},timers:[],fx:function(a,b,d){this.options=b;this.elem=a;this.prop=d;if(!b.orig)b.orig={}}});c.fx.prototype={update:function(){this.options.step&&this.options.step.call(this.elem,this.now,this);(c.fx.step[this.prop]||c.fx.step._default)(this)},cur:function(){if(this.elem[this.prop]!=null&&(!this.elem.style||this.elem.style[this.prop]==null))return this.elem[this.prop];var a=parseFloat(c.css(this.elem,this.prop));return a&&a>-1E4?a:0},custom:function(a,b,d){function e(l){return f.step(l)}
+var f=this,h=c.fx;this.startTime=c.now();this.start=a;this.end=b;this.unit=d||this.unit||"px";this.now=this.start;this.pos=this.state=0;e.elem=this.elem;if(e()&&c.timers.push(e)&&!ba)ba=setInterval(h.tick,h.interval)},show:function(){this.options.orig[this.prop]=c.style(this.elem,this.prop);this.options.show=true;this.custom(this.prop==="width"||this.prop==="height"?1:0,this.cur());c(this.elem).show()},hide:function(){this.options.orig[this.prop]=c.style(this.elem,this.prop);this.options.hide=true;
+this.custom(this.cur(),0)},step:function(a){var b=c.now(),d=true;if(a||b>=this.options.duration+this.startTime){this.now=this.end;this.pos=this.state=1;this.update();this.options.curAnim[this.prop]=true;for(var e in this.options.curAnim)if(this.options.curAnim[e]!==true)d=false;if(d){if(this.options.overflow!=null&&!c.support.shrinkWrapBlocks){var f=this.elem,h=this.options;c.each(["","X","Y"],function(k,o){f.style["overflow"+o]=h.overflow[k]})}this.options.hide&&c(this.elem).hide();if(this.options.hide||
+this.options.show)for(var l in this.options.curAnim)c.style(this.elem,l,this.options.orig[l]);this.options.complete.call(this.elem)}return false}else{a=b-this.startTime;this.state=a/this.options.duration;b=this.options.easing||(c.easing.swing?"swing":"linear");this.pos=c.easing[this.options.specialEasing&&this.options.specialEasing[this.prop]||b](this.state,a,0,1,this.options.duration);this.now=this.start+(this.end-this.start)*this.pos;this.update()}return true}};c.extend(c.fx,{tick:function(){for(var a=
+c.timers,b=0;b<a.length;b++)a[b]()||a.splice(b--,1);a.length||c.fx.stop()},interval:13,stop:function(){clearInterval(ba);ba=null},speeds:{slow:600,fast:200,_default:400},step:{opacity:function(a){c.style(a.elem,"opacity",a.now)},_default:function(a){if(a.elem.style&&a.elem.style[a.prop]!=null)a.elem.style[a.prop]=(a.prop==="width"||a.prop==="height"?Math.max(0,a.now):a.now)+a.unit;else a.elem[a.prop]=a.now}}});if(c.expr&&c.expr.filters)c.expr.filters.animated=function(a){return c.grep(c.timers,function(b){return a===
+b.elem}).length};var xb=/^t(?:able|d|h)$/i,Ia=/^(?:body|html)$/i;c.fn.offset="getBoundingClientRect"in t.documentElement?function(a){var b=this[0],d;if(a)return this.each(function(l){c.offset.setOffset(this,a,l)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);try{d=b.getBoundingClientRect()}catch(e){}var f=b.ownerDocument,h=f.documentElement;if(!d||!c.contains(h,b))return d||{top:0,left:0};b=f.body;f=fa(f);return{top:d.top+(f.pageYOffset||c.support.boxModel&&
+h.scrollTop||b.scrollTop)-(h.clientTop||b.clientTop||0),left:d.left+(f.pageXOffset||c.support.boxModel&&h.scrollLeft||b.scrollLeft)-(h.clientLeft||b.clientLeft||0)}}:function(a){var b=this[0];if(a)return this.each(function(x){c.offset.setOffset(this,a,x)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);c.offset.initialize();var d,e=b.offsetParent,f=b.ownerDocument,h=f.documentElement,l=f.body;d=(f=f.defaultView)?f.getComputedStyle(b,null):b.currentStyle;
+for(var k=b.offsetTop,o=b.offsetLeft;(b=b.parentNode)&&b!==l&&b!==h;){if(c.offset.supportsFixedPosition&&d.position==="fixed")break;d=f?f.getComputedStyle(b,null):b.currentStyle;k-=b.scrollTop;o-=b.scrollLeft;if(b===e){k+=b.offsetTop;o+=b.offsetLeft;if(c.offset.doesNotAddBorder&&!(c.offset.doesAddBorderForTableAndCells&&xb.test(b.nodeName))){k+=parseFloat(d.borderTopWidth)||0;o+=parseFloat(d.borderLeftWidth)||0}e=b.offsetParent}if(c.offset.subtractsBorderForOverflowNotVisible&&d.overflow!=="visible"){k+=
+parseFloat(d.borderTopWidth)||0;o+=parseFloat(d.borderLeftWidth)||0}d=d}if(d.position==="relative"||d.position==="static"){k+=l.offsetTop;o+=l.offsetLeft}if(c.offset.supportsFixedPosition&&d.position==="fixed"){k+=Math.max(h.scrollTop,l.scrollTop);o+=Math.max(h.scrollLeft,l.scrollLeft)}return{top:k,left:o}};c.offset={initialize:function(){var a=t.body,b=t.createElement("div"),d,e,f,h=parseFloat(c.css(a,"marginTop"))||0;c.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",
+height:"1px",visibility:"hidden"});b.innerHTML="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";a.insertBefore(b,a.firstChild);d=b.firstChild;e=d.firstChild;f=d.nextSibling.firstChild.firstChild;this.doesNotAddBorder=e.offsetTop!==5;this.doesAddBorderForTableAndCells=
+f.offsetTop===5;e.style.position="fixed";e.style.top="20px";this.supportsFixedPosition=e.offsetTop===20||e.offsetTop===15;e.style.position=e.style.top="";d.style.overflow="hidden";d.style.position="relative";this.subtractsBorderForOverflowNotVisible=e.offsetTop===-5;this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==h;a.removeChild(b);c.offset.initialize=c.noop},bodyOffset:function(a){var b=a.offsetTop,d=a.offsetLeft;c.offset.initialize();if(c.offset.doesNotIncludeMarginInBodyOffset){b+=parseFloat(c.css(a,
+"marginTop"))||0;d+=parseFloat(c.css(a,"marginLeft"))||0}return{top:b,left:d}},setOffset:function(a,b,d){var e=c.css(a,"position");if(e==="static")a.style.position="relative";var f=c(a),h=f.offset(),l=c.css(a,"top"),k=c.css(a,"left"),o=e==="absolute"&&c.inArray("auto",[l,k])>-1;e={};var x={};if(o)x=f.position();l=o?x.top:parseInt(l,10)||0;k=o?x.left:parseInt(k,10)||0;if(c.isFunction(b))b=b.call(a,d,h);if(b.top!=null)e.top=b.top-h.top+l;if(b.left!=null)e.left=b.left-h.left+k;"using"in b?b.using.call(a,
+e):f.css(e)}};c.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),d=this.offset(),e=Ia.test(b[0].nodeName)?{top:0,left:0}:b.offset();d.top-=parseFloat(c.css(a,"marginTop"))||0;d.left-=parseFloat(c.css(a,"marginLeft"))||0;e.top+=parseFloat(c.css(b[0],"borderTopWidth"))||0;e.left+=parseFloat(c.css(b[0],"borderLeftWidth"))||0;return{top:d.top-e.top,left:d.left-e.left}},offsetParent:function(){return this.map(function(){for(var a=this.offsetParent||t.body;a&&!Ia.test(a.nodeName)&&
+c.css(a,"position")==="static";)a=a.offsetParent;return a})}});c.each(["Left","Top"],function(a,b){var d="scroll"+b;c.fn[d]=function(e){var f=this[0],h;if(!f)return null;if(e!==B)return this.each(function(){if(h=fa(this))h.scrollTo(!a?e:c(h).scrollLeft(),a?e:c(h).scrollTop());else this[d]=e});else return(h=fa(f))?"pageXOffset"in h?h[a?"pageYOffset":"pageXOffset"]:c.support.boxModel&&h.document.documentElement[d]||h.document.body[d]:f[d]}});c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();
+c.fn["inner"+b]=function(){return this[0]?parseFloat(c.css(this[0],d,"padding")):null};c.fn["outer"+b]=function(e){return this[0]?parseFloat(c.css(this[0],d,e?"margin":"border")):null};c.fn[d]=function(e){var f=this[0];if(!f)return e==null?null:this;if(c.isFunction(e))return this.each(function(l){var k=c(this);k[d](e.call(this,l,k[d]()))});if(c.isWindow(f))return f.document.compatMode==="CSS1Compat"&&f.document.documentElement["client"+b]||f.document.body["client"+b];else if(f.nodeType===9)return Math.max(f.documentElement["client"+
+b],f.body["scroll"+b],f.documentElement["scroll"+b],f.body["offset"+b],f.documentElement["offset"+b]);else if(e===B){f=c.css(f,d);var h=parseFloat(f);return c.isNaN(h)?f:h}else return this.css(d,typeof e==="string"?e:e+"px")}})})(window);
--- /dev/null
+\feff/*!
+ * jQuery blockUI plugin
+ * Version 2.37 (29-JAN-2011)
+ * @requires jQuery v1.2.3 or later
+ *
+ * Examples at: http://malsup.com/jquery/block/
+ * Copyright (c) 2007-2010 M. Alsup
+ * Dual licensed under the MIT and GPL licenses:
+ * http://www.opensource.org/licenses/mit-license.php
+ * http://www.gnu.org/licenses/gpl.html
+ *
+ * Thanks to Amir-Hossein Sobhi for some excellent contributions!
+ */
+
+;(function($) {
+
+if (/1\.(0|1|2)\.(0|1|2)/.test($.fn.jquery) || /^1.1/.test($.fn.jquery)) {
+ alert('blockUI requires jQuery v1.2.3 or later! You are using v' + $.fn.jquery);
+ return;
+}
+
+$.fn._fadeIn = $.fn.fadeIn;
+
+var noOp = function() {};
+
+// this bit is to ensure we don't call setExpression when we shouldn't (with extra muscle to handle
+// retarded userAgent strings on Vista)
+var mode = document.documentMode || 0;
+var setExpr = $.browser.msie && (($.browser.version < 8 && !mode) || mode < 8);
+var ie6 = $.browser.msie && /MSIE 6.0/.test(navigator.userAgent) && !mode;
+
+// global $ methods for blocking/unblocking the entire page
+$.blockUI = function(opts) { install(window, opts); };
+$.unblockUI = function(opts) { remove(window, opts); };
+
+// convenience method for quick growl-like notifications (http://www.google.com/search?q=growl)
+$.growlUI = function(title, message, timeout, onClose) {
+ var $m = $('<div class="growlUI"></div>');
+ if (title) $m.append('<h1>'+title+'</h1>');
+ if (message) $m.append('<h2>'+message+'</h2>');
+ if (timeout == undefined) timeout = 3000;
+ $.blockUI({
+ message: $m, fadeIn: 700, fadeOut: 1000, centerY: false,
+ timeout: timeout, showOverlay: false,
+ onUnblock: onClose,
+ css: $.blockUI.defaults.growlCSS
+ });
+};
+
+// plugin method for blocking element content
+$.fn.block = function(opts) {
+ return this.unblock({ fadeOut: 0 }).each(function() {
+ if ($.css(this,'position') == 'static')
+ this.style.position = 'relative';
+ if ($.browser.msie)
+ this.style.zoom = 1; // force 'hasLayout'
+ install(this, opts);
+ });
+};
+
+// plugin method for unblocking element content
+$.fn.unblock = function(opts) {
+ return this.each(function() {
+ remove(this, opts);
+ });
+};
+
+$.blockUI.version = 2.37; // 2nd generation blocking at no extra cost!
+
+// override these in your code to change the default behavior and style
+$.blockUI.defaults = {
+ // message displayed when blocking (use null for no message)
+ message: '<h1>Please wait...</h1>',
+
+ title: null, // title string; only used when theme == true
+ draggable: true, // only used when theme == true (requires jquery-ui.js to be loaded)
+
+ theme: false, // set to true to use with jQuery UI themes
+
+ // styles for the message when blocking; if you wish to disable
+ // these and use an external stylesheet then do this in your code:
+ // $.blockUI.defaults.css = {};
+ css: {
+ padding: 0,
+ margin: 0,
+ width: '30%',
+ top: '40%',
+ left: '35%',
+ textAlign: 'center',
+ color: '#000',
+ border: '3px solid #aaa',
+ backgroundColor:'#fff',
+ cursor: 'wait'
+ },
+
+ // minimal style set used when themes are used
+ themedCSS: {
+ width: '30%',
+ top: '40%',
+ left: '35%'
+ },
+
+ // styles for the overlay
+ overlayCSS: {
+ backgroundColor: '#000',
+ opacity: 0.6,
+ cursor: 'wait'
+ },
+
+ // styles applied when using $.growlUI
+ growlCSS: {
+ width: '350px',
+ top: '10px',
+ left: '',
+ right: '10px',
+ border: 'none',
+ padding: '5px',
+ opacity: 0.6,
+ cursor: 'default',
+ color: '#fff',
+ backgroundColor: '#000',
+ '-webkit-border-radius': '10px',
+ '-moz-border-radius': '10px',
+ 'border-radius': '10px'
+ },
+
+ // IE issues: 'about:blank' fails on HTTPS and javascript:false is s-l-o-w
+ // (hat tip to Jorge H. N. de Vasconcelos)
+ iframeSrc: /^https/i.test(window.location.href || '') ? 'javascript:false' : 'about:blank',
+
+ // force usage of iframe in non-IE browsers (handy for blocking applets)
+ forceIframe: false,
+
+ // z-index for the blocking overlay
+ baseZ: 1000,
+
+ // set these to true to have the message automatically centered
+ centerX: true, // <-- only effects element blocking (page block controlled via css above)
+ centerY: true,
+
+ // allow body element to be stetched in ie6; this makes blocking look better
+ // on "short" pages. disable if you wish to prevent changes to the body height
+ allowBodyStretch: true,
+
+ // enable if you want key and mouse events to be disabled for content that is blocked
+ bindEvents: true,
+
+ // be default blockUI will supress tab navigation from leaving blocking content
+ // (if bindEvents is true)
+ constrainTabKey: true,
+
+ // fadeIn time in millis; set to 0 to disable fadeIn on block
+ fadeIn: 200,
+
+ // fadeOut time in millis; set to 0 to disable fadeOut on unblock
+ fadeOut: 400,
+
+ // time in millis to wait before auto-unblocking; set to 0 to disable auto-unblock
+ timeout: 0,
+
+ // disable if you don't want to show the overlay
+ showOverlay: true,
+
+ // if true, focus will be placed in the first available input field when
+ // page blocking
+ focusInput: true,
+
+ // suppresses the use of overlay styles on FF/Linux (due to performance issues with opacity)
+ applyPlatformOpacityRules: true,
+
+ // callback method invoked when fadeIn has completed and blocking message is visible
+ onBlock: null,
+
+ // callback method invoked when unblocking has completed; the callback is
+ // passed the element that has been unblocked (which is the window object for page
+ // blocks) and the options that were passed to the unblock call:
+ // onUnblock(element, options)
+ onUnblock: null,
+
+ // don't ask; if you really must know: http://groups.google.com/group/jquery-en/browse_thread/thread/36640a8730503595/2f6a79a77a78e493#2f6a79a77a78e493
+ quirksmodeOffsetHack: 4,
+
+ // class name of the message block
+ blockMsgClass: 'blockMsg'
+};
+
+// private data and functions follow...
+
+var pageBlock = null;
+var pageBlockEls = [];
+
+function install(el, opts) {
+ var full = (el == window);
+ var msg = opts && opts.message !== undefined ? opts.message : undefined;
+ opts = $.extend({}, $.blockUI.defaults, opts || {});
+ opts.overlayCSS = $.extend({}, $.blockUI.defaults.overlayCSS, opts.overlayCSS || {});
+ var css = $.extend({}, $.blockUI.defaults.css, opts.css || {});
+ var themedCSS = $.extend({}, $.blockUI.defaults.themedCSS, opts.themedCSS || {});
+ msg = msg === undefined ? opts.message : msg;
+
+ // remove the current block (if there is one)
+ if (full && pageBlock)
+ remove(window, {fadeOut:0});
+
+ // if an existing element is being used as the blocking content then we capture
+ // its current place in the DOM (and current display style) so we can restore
+ // it when we unblock
+ if (msg && typeof msg != 'string' && (msg.parentNode || msg.jquery)) {
+ var node = msg.jquery ? msg[0] : msg;
+ var data = {};
+ $(el).data('blockUI.history', data);
+ data.el = node;
+ data.parent = node.parentNode;
+ data.display = node.style.display;
+ data.position = node.style.position;
+ if (data.parent)
+ data.parent.removeChild(node);
+ }
+
+ var z = opts.baseZ;
+
+ // blockUI uses 3 layers for blocking, for simplicity they are all used on every platform;
+ // layer1 is the iframe layer which is used to supress bleed through of underlying content
+ // layer2 is the overlay layer which has opacity and a wait cursor (by default)
+ // layer3 is the message content that is displayed while blocking
+
+ var lyr1 = ($.browser.msie || opts.forceIframe)
+ ? $('<iframe class="blockUI" style="z-index:'+ (z++) +';display:none;border:none;margin:0;padding:0;position:absolute;width:100%;height:100%;top:0;left:0" src="'+opts.iframeSrc+'"></iframe>')
+ : $('<div class="blockUI" style="display:none"></div>');
+ var lyr2 = $('<div class="blockUI blockOverlay" style="z-index:'+ (z++) +';display:none;border:none;margin:0;padding:0;width:100%;height:100%;top:0;left:0"></div>');
+
+ var lyr3, s;
+ if (opts.theme && full) {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockPage ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:fixed">' +
+ '<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title || ' ')+'</div>' +
+ '<div class="ui-widget-content ui-dialog-content"></div>' +
+ '</div>';
+ }
+ else if (opts.theme) {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockElement ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:absolute">' +
+ '<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title || ' ')+'</div>' +
+ '<div class="ui-widget-content ui-dialog-content"></div>' +
+ '</div>';
+ }
+ else if (full) {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockPage" style="z-index:'+z+';display:none;position:fixed"></div>';
+ }
+ else {
+ s = '<div class="blockUI ' + opts.blockMsgClass + ' blockElement" style="z-index:'+z+';display:none;position:absolute"></div>';
+ }
+ lyr3 = $(s);
+
+ // if we have a message, style it
+ if (msg) {
+ if (opts.theme) {
+ lyr3.css(themedCSS);
+ lyr3.addClass('ui-widget-content');
+ }
+ else
+ lyr3.css(css);
+ }
+
+ // style the overlay
+ if (!opts.applyPlatformOpacityRules || !($.browser.mozilla && /Linux/.test(navigator.platform)))
+ lyr2.css(opts.overlayCSS);
+ lyr2.css('position', full ? 'fixed' : 'absolute');
+
+ // make iframe layer transparent in IE
+ if ($.browser.msie || opts.forceIframe)
+ lyr1.css('opacity',0.0);
+
+ //$([lyr1[0],lyr2[0],lyr3[0]]).appendTo(full ? 'body' : el);
+ var layers = [lyr1,lyr2,lyr3], $par = full ? $('body') : $(el);
+ $.each(layers, function() {
+ this.appendTo($par);
+ });
+
+ if (opts.theme && opts.draggable && $.fn.draggable) {
+ lyr3.draggable({
+ handle: '.ui-dialog-titlebar',
+ cancel: 'li'
+ });
+ }
+
+ // ie7 must use absolute positioning in quirks mode and to account for activex issues (when scrolling)
+ var expr = setExpr && (!$.boxModel || $('object,embed', full ? null : el).length > 0);
+ if (ie6 || expr) {
+ // give body 100% height
+ if (full && opts.allowBodyStretch && $.boxModel)
+ $('html,body').css('height','100%');
+
+ // fix ie6 issue when blocked element has a border width
+ if ((ie6 || !$.boxModel) && !full) {
+ var t = sz(el,'borderTopWidth'), l = sz(el,'borderLeftWidth');
+ var fixT = t ? '(0 - '+t+')' : 0;
+ var fixL = l ? '(0 - '+l+')' : 0;
+ }
+
+ // simulate fixed position
+ $.each([lyr1,lyr2,lyr3], function(i,o) {
+ var s = o[0].style;
+ s.position = 'absolute';
+ if (i < 2) {
+ full ? s.setExpression('height','Math.max(document.body.scrollHeight, document.body.offsetHeight) - (jQuery.boxModel?0:'+opts.quirksmodeOffsetHack+') + "px"')
+ : s.setExpression('height','this.parentNode.offsetHeight + "px"');
+ full ? s.setExpression('width','jQuery.boxModel && document.documentElement.clientWidth || document.body.clientWidth + "px"')
+ : s.setExpression('width','this.parentNode.offsetWidth + "px"');
+ if (fixL) s.setExpression('left', fixL);
+ if (fixT) s.setExpression('top', fixT);
+ }
+ else if (opts.centerY) {
+ if (full) s.setExpression('top','(document.documentElement.clientHeight || document.body.clientHeight) / 2 - (this.offsetHeight / 2) + (blah = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + "px"');
+ s.marginTop = 0;
+ }
+ else if (!opts.centerY && full) {
+ var top = (opts.css && opts.css.top) ? parseInt(opts.css.top) : 0;
+ var expression = '((document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + '+top+') + "px"';
+ s.setExpression('top',expression);
+ }
+ });
+ }
+
+ // show the message
+ if (msg) {
+ if (opts.theme)
+ lyr3.find('.ui-widget-content').append(msg);
+ else
+ lyr3.append(msg);
+ if (msg.jquery || msg.nodeType)
+ $(msg).show();
+ }
+
+ if (($.browser.msie || opts.forceIframe) && opts.showOverlay)
+ lyr1.show(); // opacity is zero
+ if (opts.fadeIn) {
+ var cb = opts.onBlock ? opts.onBlock : noOp;
+ var cb1 = (opts.showOverlay && !msg) ? cb : noOp;
+ var cb2 = msg ? cb : noOp;
+ if (opts.showOverlay)
+ lyr2._fadeIn(opts.fadeIn, cb1);
+ if (msg)
+ lyr3._fadeIn(opts.fadeIn, cb2);
+ }
+ else {
+ if (opts.showOverlay)
+ lyr2.show();
+ if (msg)
+ lyr3.show();
+ if (opts.onBlock)
+ opts.onBlock();
+ }
+
+ // bind key and mouse events
+ bind(1, el, opts);
+
+ if (full) {
+ pageBlock = lyr3[0];
+ pageBlockEls = $(':input:enabled:visible',pageBlock);
+ if (opts.focusInput)
+ setTimeout(focus, 20);
+ }
+ else
+ center(lyr3[0], opts.centerX, opts.centerY);
+
+ if (opts.timeout) {
+ // auto-unblock
+ var to = setTimeout(function() {
+ full ? $.unblockUI(opts) : $(el).unblock(opts);
+ }, opts.timeout);
+ $(el).data('blockUI.timeout', to);
+ }
+};
+
+// remove the block
+function remove(el, opts) {
+ var full = (el == window);
+ var $el = $(el);
+ var data = $el.data('blockUI.history');
+ var to = $el.data('blockUI.timeout');
+ if (to) {
+ clearTimeout(to);
+ $el.removeData('blockUI.timeout');
+ }
+ opts = $.extend({}, $.blockUI.defaults, opts || {});
+ bind(0, el, opts); // unbind events
+
+ var els;
+ if (full) // crazy selector to handle odd field errors in ie6/7
+ els = $('body').children().filter('.blockUI').add('body > .blockUI');
+ else
+ els = $('.blockUI', el);
+
+ if (full)
+ pageBlock = pageBlockEls = null;
+
+ if (opts.fadeOut) {
+ els.fadeOut(opts.fadeOut);
+ setTimeout(function() { reset(els,data,opts,el); }, opts.fadeOut);
+ }
+ else
+ reset(els, data, opts, el);
+};
+
+// move blocking element back into the DOM where it started
+function reset(els,data,opts,el) {
+ els.each(function(i,o) {
+ // remove via DOM calls so we don't lose event handlers
+ if (this.parentNode)
+ this.parentNode.removeChild(this);
+ });
+
+ if (data && data.el) {
+ data.el.style.display = data.display;
+ data.el.style.position = data.position;
+ if (data.parent)
+ data.parent.appendChild(data.el);
+ $(el).removeData('blockUI.history');
+ }
+
+ if (typeof opts.onUnblock == 'function')
+ opts.onUnblock(el,opts);
+};
+
+// bind/unbind the handler
+function bind(b, el, opts) {
+ var full = el == window, $el = $(el);
+
+ // don't bother unbinding if there is nothing to unbind
+ if (!b && (full && !pageBlock || !full && !$el.data('blockUI.isBlocked')))
+ return;
+ if (!full)
+ $el.data('blockUI.isBlocked', b);
+
+ // don't bind events when overlay is not in use or if bindEvents is false
+ if (!opts.bindEvents || (b && !opts.showOverlay))
+ return;
+
+ // bind anchors and inputs for mouse and key events
+ var events = 'mousedown mouseup keydown keypress';
+ b ? $(document).bind(events, opts, handler) : $(document).unbind(events, handler);
+
+// former impl...
+// var $e = $('a,:input');
+// b ? $e.bind(events, opts, handler) : $e.unbind(events, handler);
+};
+
+// event handler to suppress keyboard/mouse events when blocking
+function handler(e) {
+ // allow tab navigation (conditionally)
+ if (e.keyCode && e.keyCode == 9) {
+ if (pageBlock && e.data.constrainTabKey) {
+ var els = pageBlockEls;
+ var fwd = !e.shiftKey && e.target === els[els.length-1];
+ var back = e.shiftKey && e.target === els[0];
+ if (fwd || back) {
+ setTimeout(function(){focus(back)},10);
+ return false;
+ }
+ }
+ }
+ var opts = e.data;
+ // allow events within the message content
+ if ($(e.target).parents('div.' + opts.blockMsgClass).length > 0)
+ return true;
+
+ // allow events for content that is not being blocked
+ return $(e.target).parents().children().filter('div.blockUI').length == 0;
+};
+
+function focus(back) {
+ if (!pageBlockEls)
+ return;
+ var e = pageBlockEls[back===true ? pageBlockEls.length-1 : 0];
+ if (e)
+ e.focus();
+};
+
+function center(el, x, y) {
+ var p = el.parentNode, s = el.style;
+ var l = ((p.offsetWidth - el.offsetWidth)/2) - sz(p,'borderLeftWidth');
+ var t = ((p.offsetHeight - el.offsetHeight)/2) - sz(p,'borderTopWidth');
+ if (x) s.left = l > 0 ? (l+'px') : '0';
+ if (y) s.top = t > 0 ? (t+'px') : '0';
+};
+
+function sz(el, p) {
+ return parseInt($.css(el,p))||0;
+};
+
+})(jQuery);
--- /dev/null
+\feff/*
+ *
+ * jQuery Timer plugin v0.1
+ * Matt Schmidt [http://www.mattptr.net]
+ *
+ * Licensed under the BSD License:
+ * http://mattptr.net/license/license.txt
+ *
+ */
+
+ jQuery.timer = function (interval, callback)
+ {
+ /**
+ *
+ * timer() provides a cleaner way to handle intervals
+ *
+ * @usage
+ * $.timer(interval, callback);
+ *
+ *
+ * @example
+ * $.timer(1000, function (timer) {
+ * alert("hello");
+ * timer.stop();
+ * });
+ * @desc Show an alert box after 1 second and stop
+ *
+ * @example
+ * var second = false;
+ * $.timer(1000, function (timer) {
+ * if (!second) {
+ * alert('First time!');
+ * second = true;
+ * timer.reset(3000);
+ * }
+ * else {
+ * alert('Second time');
+ * timer.stop();
+ * }
+ * });
+ * @desc Show an alert box after 1 second and show another after 3 seconds
+ *
+ *
+ */
+
+ var interval = interval || 100;
+
+ if (!callback)
+ return false;
+
+ _timer = function (interval, callback) {
+ this.stop = function () {
+ clearInterval(self.id);
+ };
+
+ this.internalCallback = function () {
+ callback(self);
+ };
+
+ this.reset = function (val) {
+ if (self.id)
+ clearInterval(self.id);
+
+ var val = val || 100;
+ this.id = setInterval(this.internalCallback, val);
+ };
+
+ this.interval = interval;
+ this.id = setInterval(this.internalCallback, this.interval);
+
+ var self = this;
+ };
+
+ return new _timer(interval, callback);
+ };
\ No newline at end of file
--- /dev/null
+/**\r
+ * Copyright 2010 Tim Down.\r
+ *\r
+ * Licensed under the Apache License, Version 2.0 (the "License");\r
+ * you may not use this file except in compliance with the License.\r
+ * You may obtain a copy of the License at\r
+ *\r
+ * http://www.apache.org/licenses/LICENSE-2.0\r
+ *\r
+ * Unless required by applicable law or agreed to in writing, software\r
+ * distributed under the License is distributed on an "AS IS" BASIS,\r
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r
+ * See the License for the specific language governing permissions and\r
+ * limitations under the License.\r
+ */\r
+var Hashtable=(function(){var p="function";var n=(typeof Array.prototype.splice==p)?function(s,r){s.splice(r,1)}:function(u,t){var s,v,r;if(t===u.length-1){u.length=t}else{s=u.slice(t+1);u.length=t;for(v=0,r=s.length;v<r;++v){u[t+v]=s[v]}}};function a(t){var r;if(typeof t=="string"){return t}else{if(typeof t.hashCode==p){r=t.hashCode();return(typeof r=="string")?r:a(r)}else{if(typeof t.toString==p){return t.toString()}else{try{return String(t)}catch(s){return Object.prototype.toString.call(t)}}}}}function g(r,s){return r.equals(s)}function e(r,s){return(typeof s.equals==p)?s.equals(r):(r===s)}function c(r){return function(s){if(s===null){throw new Error("null is not a valid "+r)}else{if(typeof s=="undefined"){throw new Error(r+" must not be undefined")}}}}var q=c("key"),l=c("value");function d(u,s,t,r){this[0]=u;this.entries=[];this.addEntry(s,t);if(r!==null){this.getEqualityFunction=function(){return r}}}var h=0,j=1,f=2;function o(r){return function(t){var s=this.entries.length,v,u=this.getEqualityFunction(t);while(s--){v=this.entries[s];if(u(t,v[0])){switch(r){case h:return true;case j:return v;case f:return[s,v[1]]}}}return false}}function k(r){return function(u){var v=u.length;for(var t=0,s=this.entries.length;t<s;++t){u[v+t]=this.entries[t][r]}}}d.prototype={getEqualityFunction:function(r){return(typeof r.equals==p)?g:e},getEntryForKey:o(j),getEntryAndIndexForKey:o(f),removeEntryForKey:function(s){var r=this.getEntryAndIndexForKey(s);if(r){n(this.entries,r[0]);return r[1]}return null},addEntry:function(r,s){this.entries[this.entries.length]=[r,s]},keys:k(0),values:k(1),getEntries:function(s){var u=s.length;for(var t=0,r=this.entries.length;t<r;++t){s[u+t]=this.entries[t].slice(0)}},containsKey:o(h),containsValue:function(s){var r=this.entries.length;while(r--){if(s===this.entries[r][1]){return true}}return false}};function m(s,t){var r=s.length,u;while(r--){u=s[r];if(t===u[0]){return r}}return null}function i(r,s){var t=r[s];return(t&&(t instanceof d))?t:null}function b(t,r){var w=this;var v=[];var u={};var x=(typeof t==p)?t:a;var s=(typeof r==p)?r:null;this.put=function(B,C){q(B);l(C);var D=x(B),E,A,z=null;E=i(u,D);if(E){A=E.getEntryForKey(B);if(A){z=A[1];A[1]=C}else{E.addEntry(B,C)}}else{E=new d(D,B,C,s);v[v.length]=E;u[D]=E}return z};this.get=function(A){q(A);var B=x(A);var C=i(u,B);if(C){var z=C.getEntryForKey(A);if(z){return z[1]}}return null};this.containsKey=function(A){q(A);var z=x(A);var B=i(u,z);return B?B.containsKey(A):false};this.containsValue=function(A){l(A);var z=v.length;while(z--){if(v[z].containsValue(A)){return true}}return false};this.clear=function(){v.length=0;u={}};this.isEmpty=function(){return !v.length};var y=function(z){return function(){var A=[],B=v.length;while(B--){v[B][z](A)}return A}};this.keys=y("keys");this.values=y("values");this.entries=y("getEntries");this.remove=function(B){q(B);var C=x(B),z,A=null;var D=i(u,C);if(D){A=D.removeEntryForKey(B);if(A!==null){if(!D.entries.length){z=m(v,C);n(v,z);delete u[C]}}}return A};this.size=function(){var A=0,z=v.length;while(z--){A+=v[z].entries.length}return A};this.each=function(C){var z=w.entries(),A=z.length,B;while(A--){B=z[A];C(B[0],B[1])}};this.putAll=function(H,C){var B=H.entries();var E,F,D,z,A=B.length;var G=(typeof C==p);while(A--){E=B[A];F=E[0];D=E[1];if(G&&(z=w.get(F))){D=C(F,z,D)}w.put(F,D)}};this.clone=function(){var z=new b(t,r);z.putAll(w);return z}}return b})();
\ No newline at end of file
--- /dev/null
+/* Jmol 12.0 script library Jmol.js 9:48 PM 1/31/2011 Bob Hanson\r
+\r
+ checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm\r
+\r
+ based on:\r
+ *\r
+ * Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org\r
+ *\r
+ * Contact: hansonr@stolaf.edu\r
+ *\r
+ * This library is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU Lesser General Public\r
+ * License as published by the Free Software Foundation; either\r
+ * version 2.1 of the License, or (at your option) any later version.\r
+ *\r
+ * This library is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+ * Lesser General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU Lesser General Public\r
+ * License along with this library; if not, write to the Free Software\r
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA\r
+ * 02111-1307 USA.\r
+ */\r
+\r
+// for documentation see www.jmol.org/jslibrary\r
+\r
+try{if(typeof(_jmol)!="undefined")exit()\r
+\r
+// place "?NOAPPLET" on your command line to check applet control action with a textarea\r
+// place "?JMOLJAR=xxxxx" to use a specific jar file\r
+\r
+// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)\r
+// angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet\r
+// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007\r
+// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007\r
+// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007\r
+// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006\r
+// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006\r
+// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006\r
+// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006\r
+// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.\r
+// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006\r
+// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006\r
+// bob hanson -- fix for iframes not available for finding applet\r
+// bob hanson -- added applet fake ?NOAPPLET URL flag\r
+// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006\r
+// used PRIOR to jmolApplet() or jmolAppletInline()\r
+// added 4th array element in jmolRadioGroup -- title\r
+// added <span> and id around link, checkbox, radio, menu\r
+// fixing AJAX loads for MSIE/Opera-Mozilla incompatibility\r
+// -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar\r
+// renamed Jmol.js for Jmol 11 distribution\r
+// -- modified jmolRestoreOrientation() to be immediate, no 1-second delay\r
+// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006\r
+// bh -- jmolCommandInput()\r
+// bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues\r
+// bh -- minor fixes suggested by Angel\r
+// bh -- adds jmolSetSyncId() and jmolGetSyncId()\r
+// bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray()\r
+// bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray()\r
+// bh 6/2008 -- adds jmolSetAppletWindow()\r
+// Angel H. 6/2008 -- added html <label> tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]\r
+// bh 7/2008 -- code fix "for(i..." not "for(var i..."\r
+// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)\r
+// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console\r
+\r
+// bh 5/2009 -- Support for XHTML using jmolSetXHTML(id)\r
+// ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax\r
+// bh 11/2009 -- care in accessing top.document\r
+// bh 12/2009 -- added jmolSetParameter(name, value)\r
+// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line\r
+// bh 12/2009 -- overhaul of target checking\r
+// bh 1/2010 -- all _xxxx() methods ALWAYS have complete argument list\r
+// bh 1/2010 -- adds option to run a JavaScript function from any Jmol control. \r
+// This is accomplished by passing an array rather than a script:\r
+// jmolHref([myfunc,"my param 1", "my param 2"], "testing")\r
+// function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}\r
+// and allows much more flexibility with responding to controls\r
+// bh 4/2010 -- added jmolSetMemoryMb(nMb)\r
+// ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag; \r
+// fix of object tag (removed classid) accounts for change of behavior in Chrome\r
+// bh 3/2011 -- added jmolLoadAjax_STOLAF_NIH\r
+\r
+var defaultdir = "."\r
+var defaultjar = "JmolApplet.jar"\r
+\r
+\r
+// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:\r
+\r
+// JMOLJAR=xxxxx.jar on the URL for this page will override\r
+// the JAR file specified in the jmolInitialize() call.\r
+\r
+// The idea is that it can be very useful to test a web page with different JAR files\r
+// Or for an expert user to substitute a signed applet for an unsigned one\r
+// so as to use a broader range of models or to create JPEG files, for example.\r
+\r
+// If the JAR file is not in the current directory (has any sort of "/" in its name)\r
+// then the user is presented with a warning and asked whether it is OK to change Jar files.\r
+// The default action, if the user just presses "OK" is to NOT allow the change. \r
+// The user must type the word "yes" in the prompt box for the change to be approved.\r
+\r
+// If you don't want people to be able to switch in their own JAR file on your page,\r
+// simply set this next line to read "var allowJMOLJAR = false".\r
+\r
+\r
+var undefined; // for IE 5 ... wherein undefined is undefined\r
+\r
+////////////////////////////////////////////////////////////////\r
+// Basic Scripting infrastruture\r
+////////////////////////////////////////////////////////////////\r
+\r
+function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {\r
+ if (_jmol.initialized)\r
+ return;\r
+ _jmol.initialized = true;\r
+ if(_jmol.jmoljar) {\r
+ var f = _jmol.jmoljar;\r
+ if (f.indexOf("/") >= 0) {\r
+ alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.")\r
+ var ok = prompt("Do you want to use applet " + f + "? ","yes or no")\r
+ if (ok == "yes") {\r
+ codebaseDirectory = f.substring(0, f.lastIndexOf("/"));\r
+ fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);\r
+ } else {\r
+ _jmolGetJarFilename(fileNameOrUseSignedApplet);\r
+ alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');\r
+ }\r
+ } else {\r
+ fileNameOrUseSignedApplet = f;\r
+ }\r
+ }\r
+ _jmolSetCodebase(codebaseDirectory);\r
+ _jmolGetJarFilename(fileNameOrUseSignedApplet);\r
+ _jmolOnloadResetForms();\r
+}\r
+\r
+function jmolSetTranslation(TF) {\r
+ _jmol.params.doTranslate = ''+TF;\r
+}\r
+\r
+function _jmolGetJarFilename(fileNameOrFlag) {\r
+ _jmol.archivePath =\r
+ (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");\r
+}\r
+\r
+function jmolSetDocument(doc) {\r
+ _jmol.currentDocument = doc;\r
+}\r
+\r
+function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {\r
+ _jmolInitCheck();\r
+ _jmol.params.boxbgcolor = boxbgcolor;\r
+ if (boxfgcolor)\r
+ _jmol.params.boxfgcolor = boxfgcolor\r
+ else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")\r
+ _jmol.params.boxfgcolor = "black";\r
+ else\r
+ _jmol.params.boxfgcolor = "white";\r
+ if (progresscolor)\r
+ _jmol.params.progresscolor = progresscolor;\r
+ if (_jmol.debugAlert)\r
+ alert(" boxbgcolor=" + _jmol.params.boxbgcolor +\r
+ " boxfgcolor=" + _jmol.params.boxfgcolor +\r
+ " progresscolor=" + _jmol.params.progresscolor);\r
+}\r
+\r
+function jmolSetAppletWindow(w) {\r
+ _jmol.appletWindow = w;\r
+}\r
+\r
+function jmolApplet(size, script, nameSuffix) {\r
+ _jmolInitCheck();\r
+ return _jmolApplet(size, null, script, nameSuffix);\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// Basic controls\r
+////////////////////////////////////////////////////////////////\r
+\r
+// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)\r
+\r
+function jmolButton(script, label, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);\r
+ label != undefined && label != null || (label = script.substring(0, 32));\r
+ ++_jmol.buttonCount;\r
+ var scriptIndex = _jmolAddScript(script);\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +\r
+ "' value='" + label +\r
+ "' onclick='_jmolClick(this," + scriptIndex + _jmol.targetText +\r
+ ")' onmouseover='_jmolMouseOver(" + scriptIndex +\r
+ ");return true' onmouseout='_jmolMouseOut()' " +\r
+ _jmol.buttonCssText + " /></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,\r
+ labelHtml, isChecked, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount);\r
+ ++_jmol.checkboxCount;\r
+ if (scriptWhenChecked == undefined || scriptWhenChecked == null ||\r
+ scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {\r
+ alert("jmolCheckbox requires two scripts");\r
+ return;\r
+ }\r
+ if (labelHtml == undefined || labelHtml == null) {\r
+ alert("jmolCheckbox requires a label");\r
+ return;\r
+ }\r
+ var indexChecked = _jmolAddScript(scriptWhenChecked);\r
+ var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);\r
+ var eospan = "</span>"\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +\r
+ "' onclick='_jmolCbClick(this," +\r
+ indexChecked + "," + indexUnchecked + _jmol.targetText +\r
+ ")' onmouseover='_jmolCbOver(this," + indexChecked + "," +\r
+ indexUnchecked +\r
+ ");return true' onmouseout='_jmolMouseOut()' " +\r
+ (isChecked ? "checked='true' " : "")+ _jmol.checkboxCssText + " />" \r
+ if (labelHtml.toLowerCase().indexOf("<td>")>=0) {\r
+ t += eospan\r
+ eospan = "";\r
+ }\r
+ t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolStartNewRadioGroup() {\r
+ ++_jmol.radioGroupCount;\r
+}\r
+\r
+function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {\r
+ /*\r
+\r
+ array: [radio1,radio2,radio3...]\r
+ where radioN = ["script","label",isSelected,"id","title"]\r
+\r
+ */\r
+\r
+ _jmolInitCheck();\r
+ var type = typeof arrayOfRadioButtons;\r
+ if (type != "object" || type == null || ! arrayOfRadioButtons.length) {\r
+ alert("invalid arrayOfRadioButtons");\r
+ return;\r
+ }\r
+ separatorHtml != undefined && separatorHtml != null || (separatorHtml = " ");\r
+ var len = arrayOfRadioButtons.length;\r
+ jmolStartNewRadioGroup();\r
+ groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));\r
+ var t = "<span id='"+(id ? id : groupName)+"'>";\r
+ for (var i = 0; i < len; ++i) {\r
+ if (i == len - 1)\r
+ separatorHtml = "";\r
+ var radio = arrayOfRadioButtons[i];\r
+ type = typeof radio;\r
+ if (type == "object") {\r
+ t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);\r
+ } else {\r
+ t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);\r
+ }\r
+ }\r
+ t+="</span>"\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+\r
+function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {\r
+ _jmolInitCheck();\r
+ if (_jmol.radioGroupCount == 0)\r
+ ++_jmol.radioGroupCount;\r
+ var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolLink(script, label, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);\r
+ label != undefined && label != null || (label = script.substring(0, 32));\r
+ ++_jmol.linkCount;\r
+ var scriptIndex = _jmolAddScript(script);\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><a name='" + id + "' id='" + id + \r
+ "' href='javascript:_jmolClick(this," + scriptIndex + _jmol.targetText + ");' onmouseover='_jmolMouseOver(" + scriptIndex +\r
+ ");return true;' onmouseout='_jmolMouseOut()' " +\r
+ _jmol.linkCssText + ">" + label + "</a></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function jmolCommandInput(label, size, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);\r
+ label != undefined && label != null || (label = "Execute");\r
+ size != undefined && !isNaN(size) || (size = 60);\r
+ ++_jmol.cmdCount;\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" + id + "' id='" + id + \r
+ "' size='"+size+"' onkeypress='_jmolCommandKeyPress(event,\""+id+"\"" + _jmol.targetText + ")'><input type=button value = '"+label+"' onclick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")' /></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+}\r
+\r
+function _jmolCommandKeyPress(e, id, target) {\r
+ var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);\r
+ if (keycode == 13) {\r
+ var inputBox = document.getElementById(id)\r
+ _jmolScriptExecute(inputBox, inputBox.value, target)\r
+ }\r
+}\r
+\r
+function _jmolScriptExecute(element,script,target) {\r
+ if (typeof(script) == "object")\r
+ script[0](element, script, target)\r
+ else\r
+ jmolScript(script, target) \r
+}\r
+\r
+function jmolMenu(arrayOfMenuItems, size, id, title) {\r
+ _jmolInitCheck();\r
+ id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);\r
+ ++_jmol.menuCount;\r
+ var type = typeof arrayOfMenuItems;\r
+ if (type != null && type == "object" && arrayOfMenuItems.length) {\r
+ var len = arrayOfMenuItems.length;\r
+ if (typeof size != "number" || size == 1)\r
+ size = null;\r
+ else if (size < 0)\r
+ size = len;\r
+ var sizeText = size ? " size='" + size + "' " : "";\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +\r
+ "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +\r
+ sizeText + _jmol.menuCssText + ">";\r
+ for (var i = 0; i < len; ++i) {\r
+ var menuItem = arrayOfMenuItems[i];\r
+ type = typeof menuItem;\r
+ var script, text;\r
+ var isSelected = undefined;\r
+ if (type == "object" && menuItem != null) {\r
+ script = menuItem[0];\r
+ text = menuItem[1];\r
+ isSelected = menuItem[2];\r
+ } else {\r
+ script = text = menuItem;\r
+ }\r
+ text != undefined && text != null || (text = script); \r
+ if (script=="#optgroup") {\r
+ t += "<optgroup label='" + text + "'>"; \r
+ } else if (script=="#optgroupEnd") {\r
+ t += "</optgroup>"; \r
+ } else { \r
+ var scriptIndex = _jmolAddScript(script);\r
+ var selectedText = isSelected ? "' selected='true'>" : "'>";\r
+ t += "<option value='" + scriptIndex + selectedText + text + "</option>";\r
+ }\r
+ }\r
+ t += "</select></span>";\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+ }\r
+}\r
+\r
+function jmolHtml(html) {\r
+ return _jmolDocumentWrite(html);\r
+}\r
+\r
+function jmolBr() {\r
+ return _jmolDocumentWrite("<br />");\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// advanced scripting functions\r
+////////////////////////////////////////////////////////////////\r
+\r
+function jmolDebugAlert(enableAlerts) {\r
+ _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)\r
+}\r
+\r
+function jmolAppletInline(size, inlineModel, script, nameSuffix) {\r
+ _jmolInitCheck();\r
+ return _jmolApplet(size, _jmolSterilizeInline(inlineModel),\r
+ script, nameSuffix);\r
+}\r
+\r
+function jmolSetTarget(targetSuffix) {\r
+ _jmol.targetSuffix = targetSuffix;\r
+ _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : ",0";\r
+}\r
+\r
+function jmolScript(script, targetSuffix) {\r
+ if (script) {\r
+ _jmolCheckBrowser();\r
+ if (targetSuffix == "all") {\r
+ with (_jmol) {\r
+ for (var i = 0; i < appletSuffixes.length; ++i) {\r
+ var applet = _jmolGetApplet(appletSuffixes[i]);\r
+ if (applet) applet.script(script);\r
+ }\r
+ }\r
+ } else {\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) applet.script(script);\r
+ }\r
+ }\r
+}\r
+\r
+function jmolLoadInline(model, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ if (typeof(model) == "string")\r
+ return applet.loadInlineString(model, "", false);\r
+ else\r
+ return applet.loadInlineArray(model, "", false);\r
+}\r
+\r
+\r
+function jmolLoadInlineScript(model, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ return applet.loadInlineString(model, script, false);\r
+}\r
+\r
+\r
+function jmolLoadInlineArray(ModelArray, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ script || (script="")\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ try {\r
+ return applet.loadInlineArray(ModelArray, script, false);\r
+ } catch (err) {\r
+ //IE 7 bug\r
+ return applet.loadInlineString(ModelArray.join("\n"), script, false);\r
+ }\r
+}\r
+\r
+function jmolAppendInlineArray(ModelArray, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ script || (script="")\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ try {\r
+ return applet.loadInlineArray(ModelArray, script, true);\r
+ } catch (err) {\r
+ //IE 7 bug\r
+ return applet.loadInlineString(ModelArray.join("\n"), script, true);\r
+ }\r
+}\r
+\r
+function jmolAppendInlineScript(model, script, targetSuffix) {\r
+ if (!model)return "ERROR: NO MODEL"\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (!applet)return "ERROR: NO APPLET"\r
+ return applet.loadInlineString(model, script, true);\r
+}\r
+\r
+function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {\r
+ if (typeof action == "string") {\r
+ action = action.toLowerCase();\r
+ action == "alert" || action == "redirect" || action == "popup" || (action = null);\r
+ }\r
+ if (typeof action != "string")\r
+ alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +\r
+ "action must be 'alert', 'redirect', or 'popup'");\r
+ else {\r
+ if (typeof urlOrMessage != "string")\r
+ alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +\r
+ "urlOrMessage must be a string");\r
+ else {\r
+ _jmol.checkBrowserAction = action;\r
+ _jmol.checkBrowserUrlOrMessage = urlOrMessage;\r
+ }\r
+ }\r
+ if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")\r
+ _jmolCheckBrowser();\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// Cascading Style Sheet Class support\r
+////////////////////////////////////////////////////////////////\r
+\r
+function jmolSetAppletCssClass(appletCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.appletCssClass = appletCssClass;\r
+ _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetButtonCssClass(buttonCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.buttonCssClass = buttonCssClass;\r
+ _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetCheckboxCssClass(checkboxCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.checkboxCssClass = checkboxCssClass;\r
+ _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetRadioCssClass(radioCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.radioCssClass = radioCssClass;\r
+ _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetLinkCssClass(linkCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.linkCssClass = linkCssClass;\r
+ _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+function jmolSetMenuCssClass(menuCssClass) {\r
+ if (_jmol.hasGetElementById) {\r
+ _jmol.menuCssClass = menuCssClass;\r
+ _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";\r
+ }\r
+}\r
+\r
+////////////////////////////////////////////////////////////////\r
+// functions for INTERNAL USE ONLY which are subject to change\r
+// use at your own risk ... you have been WARNED!\r
+////////////////////////////////////////////////////////////////\r
+var _jmol = {\r
+ currentDocument: document,\r
+\r
+ debugAlert: false,\r
+ \r
+ codebase: "",\r
+ modelbase: ".",\r
+ \r
+ appletCount: 0,\r
+ appletSuffixes: [],\r
+ appletWindow: null,\r
+ allowedJmolSize: [25, 2048, 300], // min, max, default (pixels)\r
+ /* By setting the _jmol.allowedJmolSize[] variable in the webpage \r
+ before calling jmolApplet(), limits for applet size can be overriden.\r
+ 2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)\r
+ */ \r
+ buttonCount: 0,\r
+ checkboxCount: 0,\r
+ linkCount: 0,\r
+ cmdCount: 0,\r
+ menuCount: 0,\r
+ radioCount: 0,\r
+ radioGroupCount: 0,\r
+ \r
+ appletCssClass: null,\r
+ appletCssText: "",\r
+ buttonCssClass: null,\r
+ buttonCssText: "",\r
+ checkboxCssClass: null,\r
+ checkboxCssText: "",\r
+ java_arguments: "-Xmx512m",\r
+ radioCssClass: null,\r
+ radioCssText: "",\r
+ linkCssClass: null,\r
+ linkCssText: "",\r
+ menuCssClass: null,\r
+ menuCssText: "",\r
+ \r
+ targetSuffix: 0,\r
+ targetText: ",0",\r
+ scripts: [""],\r
+ params: {\r
+ syncId: ("" + Math.random()).substring(3),\r
+ progressbar: "true",\r
+ progresscolor: "blue",\r
+ boxbgcolor: "black",\r
+ boxfgcolor: "white",\r
+ boxmessage: "Downloading JmolApplet ..."\r
+ },\r
+ ua: navigator.userAgent.toLowerCase(),\r
+ // uaVersion: parseFloat(navigator.appVersion), // not used\r
+ \r
+ os: "unknown",\r
+ browser: "unknown",\r
+ browserVersion: 0,\r
+ hasGetElementById: !!document.getElementById,\r
+ isJavaEnabled: navigator.javaEnabled(),\r
+ // isNetscape47Win: false, // not used, N4.7 is no longer supported even for detection\r
+ useIEObject: false,\r
+ useHtml4Object: false,\r
+ \r
+ windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",\r
+ windowsCabUrl:\r
+ "http://java.sun.com/update/1.6.0/jinstall-6u22-windows-i586.cab",\r
+\r
+ isBrowserCompliant: false,\r
+ isJavaCompliant: false,\r
+ isFullyCompliant: false,\r
+\r
+ initialized: false,\r
+ initChecked: false,\r
+ \r
+ browserChecked: false,\r
+ checkBrowserAction: "alert",\r
+ checkBrowserUrlOrMessage: null,\r
+\r
+ archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar\r
+\r
+ previousOnloadHandler: null,\r
+\r
+ jmoljar: null, \r
+ useNoApplet: false,\r
+\r
+ ready: {}\r
+}\r
+\r
+with (_jmol) {\r
+ function _jmolTestUA(candidate) {\r
+ var ua = _jmol.ua;\r
+ var index = ua.indexOf(candidate);\r
+ if (index < 0)\r
+ return false;\r
+ _jmol.browser = candidate;\r
+ _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));\r
+ return true;\r
+ }\r
+ \r
+ function _jmolTestOS(candidate) {\r
+ if (_jmol.ua.indexOf(candidate) < 0)\r
+ return false;\r
+ _jmol.os = candidate;\r
+ return true;\r
+ }\r
+ \r
+ _jmolTestUA("konqueror") ||\r
+ _jmolTestUA("webkit") ||\r
+ _jmolTestUA("omniweb") ||\r
+ _jmolTestUA("opera") ||\r
+ _jmolTestUA("webtv") ||\r
+ _jmolTestUA("icab") ||\r
+ _jmolTestUA("msie") ||\r
+ (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); //Netscape, Mozilla, Seamonkey, Firefox and anything assimilated\r
+ \r
+ _jmolTestOS("linux") ||\r
+ _jmolTestOS("unix") ||\r
+ _jmolTestOS("mac") ||\r
+ _jmolTestOS("win");\r
+\r
+ /* not used:\r
+ isNetscape47Win = (os == "win" && browser == "mozilla" &&\r
+ browserVersion >= 4.78 && browserVersion <= 4.8);\r
+ */\r
+\r
+ if (os == "win") {\r
+ isBrowserCompliant = hasGetElementById;\r
+ } else if (os == "mac") { // mac is the problem child :-(\r
+ if (browser == "mozilla" && browserVersion >= 5) {\r
+ // miguel 2004 11 17\r
+ // checking the plugins array does not work because\r
+ // Netscape 7.2 OS X still has Java 1.3.1 listed even though\r
+ // javaplugin.sf.net is installed to upgrade to 1.4.2\r
+ eval("try {var v = java.lang.System.getProperty('java.version');" +\r
+ " _jmol.isBrowserCompliant = v >= '1.4.2';" +\r
+ " } catch (e) { }");\r
+ } else if (browser == "opera" && browserVersion <= 7.54) {\r
+ isBrowserCompliant = false;\r
+ } else {\r
+ isBrowserCompliant = hasGetElementById &&\r
+ !((browser == "msie") ||\r
+ (browser == "webkit" && browserVersion < 125.12));\r
+ }\r
+ } else if (os == "linux" || os == "unix") {\r
+ if (browser == "konqueror" && browserVersion <= 3.3)\r
+ isBrowserCompliant = false;\r
+ else\r
+ isBrowserCompliant = hasGetElementById;\r
+ } else { // other OS\r
+ isBrowserCompliant = hasGetElementById;\r
+ }\r
+\r
+ // possibly more checks in the future for this\r
+ isJavaCompliant = isJavaEnabled;\r
+\r
+ isFullyCompliant = isBrowserCompliant && isJavaCompliant;\r
+\r
+ useIEObject = (os == "win" && browser == "msie" && browserVersion >= 5.5);\r
+ useHtml4Object =\r
+ (browser == "mozilla" && browserVersion >= 5) ||\r
+ (browser == "opera" && browserVersion >= 8) ||\r
+ (browser == "webkit" && browserVersion >= 412.2);\r
+ try {\r
+ if (top.location.search.indexOf("JMOLJAR=")>=0)\r
+ jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];\r
+ } catch(e) {\r
+ // can't access top.location\r
+ }\r
+ try {\r
+ useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);\r
+ } catch(e) {\r
+ // can't access top.document\r
+ }\r
+}\r
+\r
+function jmolSetMemoryMb(nMb) {\r
+ _jmol.java_arguments = "-Xmx" + Math.round(nMb) + "m"\r
+}\r
+\r
+function jmolSetParameter(name,value) {\r
+ _jmol.params[name] = value\r
+}\r
+\r
+function jmolSetCallback(callbackName,funcName) {\r
+ _jmol.params[callbackName] = funcName\r
+}\r
+\r
+ try {\r
+// note this is done FIRST, so it cannot override a setting done by the developer\r
+ if (top.location.search.indexOf("PARAMS=")>=0) {\r
+ var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");\r
+ for (var i = 0; i < pars.length; i++) {\r
+ var p = pars[i].split(":");\r
+ jmolSetParameter(p[0],p[1]);\r
+ }\r
+ }\r
+ } catch(e) {\r
+ // can't access top.location\r
+ }\r
+\r
+function jmolSetSyncId(n) {\r
+ return _jmol.params["syncId"] = n\r
+}\r
+\r
+function jmolGetSyncId() {\r
+ return _jmol.params["syncId"]\r
+}\r
+\r
+function jmolSetLogLevel(n) {\r
+ _jmol.params.logLevel = ''+n;\r
+}\r
+\r
+ /* AngelH, mar2007:\r
+ By (re)setting these variables in the webpage before calling jmolApplet(), \r
+ a custom message can be provided (e.g. localized for user's language) when no Java is installed.\r
+ */\r
+if (noJavaMsg==undefined) var noJavaMsg = \r
+ "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +\r
+ "Check the warning message from your browser and/or enable Java applets in<br />\n" +\r
+ "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";\r
+if (noJavaMsg2==undefined) var noJavaMsg2 = \r
+ "You do not have the<br />\n" +\r
+ "Java Runtime Environment<br />\n" +\r
+ "installed for applet support.<br />\n" +\r
+ "Visit <a href='http://www.java.com'>www.java.com</a>";\r
+function _jmolApplet(size, inlineModel, script, nameSuffix) {\r
+ /* AngelH, mar2007\r
+ Fixed percent / pixel business, to avoid browser errors:\r
+ put "px" where needed, avoid where not.\r
+\r
+ Bob Hanson, 1/2010\r
+ Fixed inline escape changing returns to | \r
+ */\r
+ with (_jmol) {\r
+ nameSuffix == undefined && (nameSuffix = appletCount);\r
+ appletSuffixes.push(nameSuffix);\r
+ ++appletCount;\r
+ script || (script = "select *");\r
+ var sz = _jmolGetAppletSize(size);\r
+ var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";\r
+ var tHeader, tFooter;\r
+ codebase || jmolInitialize(".");\r
+ if (useIEObject || useHtml4Object) {\r
+ params.archive = archivePath;\r
+ params.mayscript = 'true';\r
+ params.codebase = codebase;\r
+ params.code = 'JmolApplet';\r
+ tHeader = \r
+ "<object name='jmolApplet" + nameSuffix +\r
+ "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +\r
+ widthAndHeight + "\n";\r
+ tFooter = "</object>";\r
+ }\r
+ if (java_arguments)\r
+ params.java_arguments = java_arguments;\r
+ if (useIEObject) { // use MSFT IE6 object tag with .cab file reference\r
+ tHeader += " classid='" + windowsClassId + "'\n" +\r
+ (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "") + ">\n";\r
+ } else if (useHtml4Object) { // use HTML4 object tag\r
+ tHeader += " type='application/x-java-applet'\n>\n";\r
+ /* " classid='java:JmolApplet'\n" + AH removed this\r
+ Chromium Issue 62076: Java Applets using an <object> with a classid paramater don't load.\r
+ http://code.google.com/p/chromium/issues/detail?id=62076\r
+ They say this is the correct behavior according to the spec, and there's no indication at this point \r
+ that WebKit will be changing the handling, so eventually Safari will acquire this behavior too.\r
+ Removing the classid parameter seems to be well tolerated by all browsers (even IE!).\r
+ */\r
+ } else { // use applet tag\r
+ tHeader = \r
+ "<applet name='jmolApplet" + nameSuffix +\r
+ "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +\r
+ widthAndHeight + "\n" +\r
+ " code='JmolApplet'" +\r
+ " archive='" + archivePath + "' codebase='" + codebase + "'\n" +\r
+ " mayscript='true'>\n";\r
+ tFooter = "</applet>";\r
+ }\r
+ var visitJava;\r
+ if (useIEObject || useHtml4Object) {\r
+ var szX = "width:" + sz[0]\r
+ if ( szX.indexOf("%")==-1 ) szX+="px" \r
+ var szY = "height:" + sz[1]\r
+ if ( szY.indexOf("%")==-1 ) szY+="px" \r
+ visitJava =\r
+ "<p style='background-color:yellow; color:black; " +\r
+ szX + ";" + szY + ";" +\r
+ // why doesn't this vertical-align work?\r
+ "text-align:center;vertical-align:middle;'>\n" +\r
+ noJavaMsg +\r
+ "</p>";\r
+ } else {\r
+ visitJava =\r
+ "<table bgcolor='yellow'><tr>" +\r
+ "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +\r
+ noJavaMsg2 +\r
+ "</font></td></tr></table>";\r
+ }\r
+ params.loadInline = (inlineModel ? inlineModel : "");\r
+ params.script = (script ? _jmolSterilizeScript(script) : "");\r
+ var t = tHeader + _jmolParams() + visitJava + tFooter;\r
+ jmolSetTarget(nameSuffix);\r
+ ready["jmolApplet" + nameSuffix] = false;\r
+ if (_jmol.debugAlert)\r
+ alert(t);\r
+ return _jmolDocumentWrite(t);\r
+ }\r
+}\r
+\r
+function _jmolParams() {\r
+ var t = "";\r
+ for (var i in _jmol.params)\r
+ if(_jmol.params[i]!="")\r
+ t+=" <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";\r
+ return t\r
+}\r
+\r
+function _jmolInitCheck() {\r
+ if (_jmol.initChecked)\r
+ return;\r
+ _jmol.initChecked = true;\r
+ jmolInitialize(defaultdir, defaultjar)\r
+}\r
+\r
+function _jmolCheckBrowser() {\r
+ with (_jmol) {\r
+ if (browserChecked)\r
+ return;\r
+ browserChecked = true;\r
+ \r
+ if (isFullyCompliant)\r
+ return true;\r
+\r
+ if (checkBrowserAction == "redirect")\r
+ location.href = checkBrowserUrlOrMessage;\r
+ else if (checkBrowserAction == "popup")\r
+ _jmolPopup(checkBrowserUrlOrMessage);\r
+ else {\r
+ var msg = checkBrowserUrlOrMessage;\r
+ if (msg == null)\r
+ msg = "Your web browser is not fully compatible with Jmol\n\n" +\r
+ "browser: " + browser +\r
+ " version: " + browserVersion +\r
+ " os: " + os +\r
+ " isBrowserCompliant: " + isBrowserCompliant +\r
+ " isJavaCompliant: " + isJavaCompliant +\r
+ "\n\n" + ua;\r
+ alert(msg);\r
+ }\r
+ }\r
+ return false;\r
+}\r
+\r
+function jmolSetXHTML(id) {\r
+ _jmol.isXHTML = true\r
+ _jmol.XhtmlElement = null\r
+ _jmol.XhtmlAppendChild = false\r
+ if (id){\r
+ _jmol.XhtmlElement = document.getElementById(id)\r
+ _jmol.XhtmlAppendChild = true\r
+ }\r
+}\r
+\r
+function _jmolDocumentWrite(text) {\r
+ if (_jmol.currentDocument) {\r
+ if (_jmol.isXHTML && !_jmol.XhtmlElement) {\r
+ var s = document.getElementsByTagName("script")\r
+ _jmol.XhtmlElement = s.item(s.length - 1)\r
+ _jmol.XhtmlAppendChild = false\r
+ }\r
+ if (_jmol.XhtmlElement) {\r
+ _jmolDomDocumentWrite(text)\r
+ } else {\r
+ _jmol.currentDocument.write(text);\r
+ }\r
+ }\r
+ return text;\r
+}\r
+\r
+function _jmolDomDocumentWrite(data) {\r
+ var pt = 0\r
+ var Ptr = []\r
+ Ptr[0] = 0\r
+ while (Ptr[0] < data.length) {\r
+ var child = _jmolGetDomElement(data, Ptr)\r
+ if (!child)break\r
+ if (_jmol.XhtmlAppendChild)\r
+ _jmol.XhtmlElement.appendChild(child)\r
+ else\r
+ _jmol.XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement); \r
+ }\r
+}\r
+function _jmolGetDomElement(data, Ptr, closetag, lvel) {\r
+ var e = document.createElement("span")\r
+ e.innerHTML = data\r
+ Ptr[0] = data.length\r
+ return e\r
+\r
+//unnecessary?\r
+\r
+ closetag || (closetag = "")\r
+ lvel || (lvel = 0)\r
+ var pt0 = Ptr[0]\r
+ var pt = pt0\r
+ while (pt < data.length && data.charAt(pt) != "<") pt++\r
+ if (pt != pt0) {\r
+ var text = data.substring(pt0, pt)\r
+ Ptr[0] = pt\r
+ return document.createTextNode(text)\r
+ } \r
+ pt0 = ++pt\r
+ var ch\r
+ while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) pt++\r
+ var tagname = data.substring(pt0, pt)\r
+ var e = (tagname == closetag || tagname == "/" ? "" \r
+ : document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)\r
+ : document.createElement(tagname));\r
+ if (ch == ">") {\r
+ Ptr[0] = ++pt\r
+ return e\r
+ }\r
+ while (pt < data.length && (ch = data.charAt(pt)) != ">") {\r
+ while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++\r
+ pt0 = pt\r
+ while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) pt++\r
+ var attrname = data.substring(pt0, pt).toLowerCase()\r
+ if (attrname && ch != "=") \r
+ e.setAttribute(attrname, "true")\r
+ while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++\r
+ if (ch == "/") {\r
+ Ptr[0] = pt + 2\r
+ return e\r
+ } else if (ch == "=") {\r
+ var quote = data.charAt(++pt)\r
+ pt0 = ++pt\r
+ while (pt < data.length && (ch = data.charAt(pt)) != quote) pt++\r
+ var attrvalue = data.substring(pt0, pt)\r
+ e.setAttribute(attrname, attrvalue)\r
+ pt++\r
+ }\r
+ }\r
+ Ptr[0] = ++pt\r
+ while (Ptr[0] < data.length) {\r
+ var child = _jmolGetDomElement(data, Ptr, "/" + tagname, lvel+1)\r
+ if (!child)break\r
+ e.appendChild(child)\r
+ }\r
+ return e\r
+}\r
+\r
+function _jmolPopup(url) {\r
+ var popup = window.open(url, "JmolPopup",\r
+ "left=150,top=150,height=400,width=600," +\r
+ "directories=yes,location=yes,menubar=yes," +\r
+ "toolbar=yes," +\r
+ "resizable=yes,scrollbars=yes,status=yes");\r
+ if (popup.focus)\r
+ poup.focus();\r
+}\r
+\r
+function _jmolReadyCallback(name) {\r
+ if (_jmol.debugAlert)\r
+ alert(name + " is ready");\r
+ _jmol.ready["" + name] = true;\r
+}\r
+\r
+function _jmolSterilizeScript(script) {\r
+ script = script.replace(/'/g, "'");\r
+ if (_jmol.debugAlert)\r
+ alert("script:\n" + script);\r
+ return script;\r
+}\r
+\r
+function _jmolSterilizeInline(model) {\r
+ model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "'");\r
+ if (_jmol.debugAlert)\r
+ alert("inline model:\n" + model);\r
+ return model;\r
+}\r
+\r
+function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {\r
+ ++_jmol.radioCount;\r
+ groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));\r
+ if (!script)\r
+ return "";\r
+ labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));\r
+ separatorHtml || (separatorHtml = "")\r
+ var scriptIndex = _jmolAddScript(script);\r
+ var eospan = "</span>"\r
+ var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" \r
+ + groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(this," +\r
+ scriptIndex + _jmol.targetText + ");return true;' onmouseover='_jmolMouseOver(" +\r
+ scriptIndex + ");return true;' onmouseout='_jmolMouseOut()' " +\r
+ (isChecked ? "checked='true' " : "") + _jmol.radioCssText + " />"\r
+ if (labelHtml.toLowerCase().indexOf("<td>")>=0) {\r
+ t += eospan\r
+ eospan = "";\r
+ }\r
+ t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan + separatorHtml;\r
+\r
+ return t;\r
+}\r
+\r
+function _jmolFindApplet(target) {\r
+ // first look for the target in the current window\r
+ var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);\r
+ // THEN look for the target in child frames\r
+ if (applet == undefined)\r
+ applet = _jmolSearchFrames(window, target);\r
+ // FINALLY look for the target in sibling frames\r
+ if (applet == undefined)\r
+ applet = _jmolSearchFrames(top, target); // look starting in top frame\r
+ return applet;\r
+}\r
+\r
+function _jmolGetApplet(targetSuffix){\r
+ var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");\r
+ var applet = _jmolFindApplet(target);\r
+ if (applet) return applet\r
+ _jmol.alerted || alert("could not find applet " + target);\r
+ _jmol.alerted = true;\r
+ return null\r
+}\r
+\r
+function _jmolSearchFrames(win, target) {\r
+ var applet;\r
+ var frames = win.frames;\r
+ if (frames && frames.length) { // look in all the frames below this window\r
+ try{\r
+ for (var i = 0; i < frames.length; ++i) {\r
+ applet = _jmolSearchFrames(frames[i], target);\r
+ if (applet)\r
+ return applet;\r
+ }\r
+ }catch(e) {\r
+ if (_jmol.debugAlert)\r
+ alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()") \r
+ }\r
+ }\r
+ return applet = _jmolFindAppletInWindow(win, target)\r
+}\r
+\r
+function _jmolFindAppletInWindow(win, target) {\r
+ var doc = win.document;\r
+ if (doc.getElementById(target))\r
+ return doc.getElementById(target);\r
+ else if (doc.applets)\r
+ return doc.applets[target];\r
+ else\r
+ return doc[target]; \r
+}\r
+\r
+function _jmolAddScript(script) {\r
+ if (!script)\r
+ return 0;\r
+ var index = _jmol.scripts.length;\r
+ _jmol.scripts[index] = script;\r
+ return index;\r
+}\r
+\r
+function _jmolClick(elementClicked, scriptIndex, targetSuffix) {\r
+ _jmol.element = elementClicked;\r
+ _jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);\r
+}\r
+\r
+function _jmolMenuSelected(menuObject, targetSuffix) {\r
+ var scriptIndex = menuObject.value;\r
+ if (scriptIndex != undefined) {\r
+ _jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);\r
+ return;\r
+ }\r
+ var len = menuObject.length;\r
+ if (typeof len == "number") {\r
+ for (var i = 0; i < len; ++i) {\r
+ if (menuObject[i].selected) {\r
+ _jmolClick(menuObject[i], menuObject[i].value, targetSuffix);\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ alert("?Que? menu selected bug #8734");\r
+}\r
+\r
+\r
+_jmol.checkboxMasters = {};\r
+_jmol.checkboxItems = {};\r
+\r
+function jmolSetCheckboxGroup(chkMaster,chkBox) {\r
+ var id = chkMaster;\r
+ if(typeof(id)=="number")id = "jmolCheckbox" + id;\r
+ chkMaster = document.getElementById(id);\r
+ if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);\r
+ var m = _jmol.checkboxMasters[id] = {};\r
+ m.chkMaster = chkMaster;\r
+ m.chkGroup = {};\r
+ for (var i = 1; i < arguments.length; i++){\r
+ var id = arguments[i];\r
+ if(typeof(id)=="number")id = "jmolCheckbox" + id;\r
+ checkboxItem = document.getElementById(id);\r
+ if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);\r
+ m.chkGroup[id] = checkboxItem;\r
+ _jmol.checkboxItems[id] = m;\r
+ }\r
+}\r
+\r
+function _jmolNotifyMaster(m){\r
+ //called when a group item is checked\r
+ var allOn = true;\r
+ var allOff = true;\r
+ for (var chkBox in m.chkGroup){\r
+ if(m.chkGroup[chkBox].checked)\r
+ allOff = false;\r
+ else\r
+ allOn = false;\r
+ }\r
+ if (allOn)m.chkMaster.checked = true; \r
+ if (allOff)m.chkMaster.checked = false;\r
+ if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])\r
+ _jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])\r
+}\r
+\r
+function _jmolNotifyGroup(m, isOn){\r
+ //called when a master item is checked\r
+ for (var chkBox in m.chkGroup){\r
+ var item = m.chkGroup[chkBox]\r
+ item.checked = isOn;\r
+ if (_jmol.checkboxMasters[item.id])\r
+ _jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)\r
+ }\r
+}\r
+\r
+function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {\r
+ _jmol.control = ckbox\r
+ _jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);\r
+ if(_jmol.checkboxMasters[ckbox.id])\r
+ _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)\r
+ if(_jmol.checkboxItems[ckbox.id])\r
+ _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])\r
+}\r
+\r
+function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {\r
+ window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];\r
+}\r
+\r
+function _jmolMouseOver(scriptIndex) {\r
+ window.status = _jmol.scripts[scriptIndex];\r
+}\r
+\r
+function _jmolMouseOut() {\r
+ window.status = " ";\r
+ return true;\r
+}\r
+\r
+function _jmolSetCodebase(codebase) {\r
+ _jmol.codebase = codebase ? codebase : ".";\r
+ if (_jmol.debugAlert)\r
+ alert("jmolCodebase=" + _jmol.codebase);\r
+}\r
+\r
+function _jmolOnloadResetForms() {\r
+ // must be evaluated ONLY once\r
+ _jmol.previousOnloadHandler = window.onload;\r
+ window.onload =\r
+ function() {\r
+ with (_jmol) {\r
+ if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {\r
+ var forms = document.forms;\r
+ for (var i = forms.length; --i >= 0; )\r
+ forms[i].reset();\r
+ }\r
+ if (previousOnloadHandler)\r
+ previousOnloadHandler();\r
+ }\r
+ }\r
+}\r
+\r
+////////////////////////////////////\r
+/////extensions for getProperty/////\r
+////////////////////////////////////\r
+\r
+\r
+function _jmolEvalJSON(s,key){\r
+ s=s+""\r
+ if(!s)return []\r
+ if(s.charAt(0)!="{"){\r
+ if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")\r
+ return s\r
+ }\r
+ var A = eval("("+s+")")\r
+ if(!A)return\r
+ if(key && A[key])A=A[key]\r
+ return A\r
+}\r
+\r
+function _jmolEnumerateObject(A,key){\r
+ var sout=""\r
+ if(typeof(A) == "string" && A!="null"){\r
+ sout+="\n"+key+"=\""+A+"\""\r
+ }else if(!isNaN(A)||A==null){\r
+ sout+="\n"+key+"="+(A+""==""?"null":A)\r
+ }else if(A.length){\r
+ sout+=key+"=[]"\r
+ for(var i=0;i<A.length;i++){\r
+ sout+="\n"\r
+ if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){\r
+ sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")\r
+ }else{\r
+ sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])\r
+ }\r
+ }\r
+ }else{\r
+ if(key != ""){\r
+ sout+=key+"={}"\r
+ key+="."\r
+ }\r
+ \r
+ for(var i in A){\r
+ sout+="\n"\r
+ if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){\r
+ sout+=_jmolEnumerateObject(A[i],key+i)\r
+ }else{\r
+ sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])\r
+ }\r
+ }\r
+ } \r
+ return sout\r
+}\r
+\r
+\r
+function _jmolSortKey0(a,b){\r
+ return (a[0]<b[0]?1:a[0]>b[0]?-1:0)\r
+}\r
+\r
+function _jmolSortMessages(A){\r
+ if(!A || typeof(A)!="object")return []\r
+ var B = []\r
+ for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]\r
+ if(B.length == 0) return\r
+ B=B.sort(_jmolSortKey0)\r
+ return B\r
+}\r
+\r
+/////////additional extensions //////////\r
+\r
+\r
+function _jmolDomScriptLoad(URL){\r
+ //open(URL) //to debug\r
+ _jmol.servercall=URL\r
+ var node = document.getElementById("_jmolScriptNode")\r
+ if (node && _jmol.browser!="msie"){\r
+ document.getElementsByTagName("HEAD")[0].removeChild(node)\r
+ node=null\r
+ }\r
+ if (node) {\r
+ node.setAttribute("src",URL)\r
+ } else {\r
+ node=document.createElement("script")\r
+ node.setAttribute("id","_jmolScriptNode")\r
+ node.setAttribute("type","text/javascript")\r
+ node.setAttribute("src",URL)\r
+ document.getElementsByTagName("HEAD")[0].appendChild(node)\r
+ }\r
+}\r
+\r
+\r
+function _jmolExtractPostData(url){\r
+ S=url.split("&POST:")\r
+ var s=""\r
+ for(var i=1;i<S.length;i++){\r
+ KV=S[i].split("=")\r
+ s+="&POSTKEY"+i+"="+KV[0]\r
+ s+="&POSTVALUE"+i+"="+KV[1]\r
+ }\r
+ return "&url="+escape(S[0])+s\r
+}\r
+\r
+function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){\r
+ //called by server, but in client\r
+ //overload this function to customize return\r
+ _jmol.remoteURL=remoteURL\r
+ isError && alert(errorMessage)\r
+ jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)\r
+}\r
+\r
+//////////user property/status functions/////////\r
+\r
+function jmolGetStatus(strStatus,targetSuffix){\r
+ return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))\r
+}\r
+\r
+function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {\r
+ return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)\r
+}\r
+\r
+function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ sValue == undefined && (sValue="");\r
+ return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")\r
+}\r
+\r
+function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {\r
+ sValue == undefined && (sValue = "")\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ try {\r
+ return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")\r
+ } catch(e) {\r
+ return ""\r
+ }\r
+}\r
+\r
+function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {\r
+ sValue == undefined && (sValue = "")\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ return (applet ? applet.getProperty(sKey,sValue) : null)\r
+}\r
+\r
+\r
+function jmolDecodeJSON(s) {\r
+ return _jmolEnumerateObject(_jmolEvalJSON(s),"")\r
+}\r
+\r
+\r
+///////// synchronous scripting ////////\r
+\r
+function jmolScriptWait(script, targetSuffix) {\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var Ret=jmolScriptWaitAsArray(script, targetSuffix)\r
+ var s = ""\r
+ for(var i=Ret.length;--i>=0;)\r
+ for(var j=0;j< Ret[i].length;j++)\r
+ s+=Ret[i][j]+"\n"\r
+ return s\r
+}\r
+\r
+function jmolScriptWaitOutput(script, targetSuffix) {\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var ret = ""\r
+ try{\r
+ if (script) {\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) ret += applet.scriptWaitOutput(script);\r
+ }\r
+ }catch(e){\r
+ }\r
+ return ret;\r
+}\r
+\r
+function jmolEvaluate(molecularMath, targetSuffix) {\r
+\r
+ //carries out molecular math on a model\r
+\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);\r
+ var s = result.replace(/\-*\d+/,"")\r
+ if (s == "" && !isNaN(parseInt(result)))return parseInt(result);\r
+ var s = result.replace(/\-*\d*\.\d*/,"")\r
+ if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);\r
+ return result;\r
+}\r
+\r
+function jmolScriptEcho(script, targetSuffix) {\r
+ // returns a newline-separated list of all echos from a script\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var Ret=jmolScriptWaitAsArray(script, targetSuffix)\r
+ var s = ""\r
+ for(var i=Ret.length;--i>=0;)\r
+ for(var j=Ret[i].length;--j>=0;)\r
+ if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"\r
+ return s.replace(/ \| /g, "\n")\r
+}\r
+\r
+\r
+function jmolScriptMessage(script, targetSuffix) {\r
+ // returns a newline-separated list of all messages from a script, ending with "script completed\n"\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var Ret=jmolScriptWaitAsArray(script, targetSuffix)\r
+ var s = ""\r
+ for(var i=Ret.length;--i>=0;)\r
+ for(var j=Ret[i].length;--j>=0;)\r
+ if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"\r
+ return s.replace(/ \| /g, "\n")\r
+}\r
+\r
+\r
+function jmolScriptWaitAsArray(script, targetSuffix) {\r
+ var ret = ""\r
+ try{\r
+ jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)\r
+ if (script) {\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) ret += applet.scriptWait(script);\r
+ ret = _jmolEvalJSON(ret,"jmolStatus")\r
+ if(typeof ret == "object")\r
+ return ret\r
+ }\r
+ }catch(e){\r
+ }\r
+ return [[ret]]\r
+}\r
+\r
+\r
+\r
+//////////// save/restore orientation /////////////\r
+\r
+function jmolSaveOrientation(id, targetSuffix) { \r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo\r
+}\r
+\r
+function jmolRestoreOrientation(id, targetSuffix) {\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var s=_jmol["savedOrientation"+id]\r
+ if (!s || s == "")return\r
+ s=s.replace(/1\.0/,"0")\r
+ return jmolScriptWait(s,targetSuffix)\r
+}\r
+\r
+function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {\r
+ arguments.length < 2 && (delay=1)\r
+ targetSuffix == undefined && (targetSuffix="0")\r
+ var s=_jmol["savedOrientation"+id]\r
+ if (!s || s == "")return\r
+ s=s.replace(/1\.0/,delay)\r
+ return jmolScriptWait(s,targetSuffix)\r
+}\r
+\r
+//////////// add parameter /////////////\r
+/*\r
+ * for adding callbacks or other parameters. Use:\r
+\r
+ jmolSetDocument(0)\r
+ var s= jmolApplet(....)\r
+ s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")\r
+ document.write(s)\r
+ jmolSetDocument(document) // if you want to then write buttons and such normally\r
+ \r
+ */\r
+\r
+function jmolAppletAddParam(appletCode,name,value){\r
+ return (value == "" ? appletCode : appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param"))\r
+}\r
+\r
+///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////\r
+\r
+function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){\r
+\r
+ _jmol.thismodel || (_jmol.thismodel = "1crn")\r
+ _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")\r
+ _jmol.RCSBserver || (_jmol.RCSBserver="http://www.rcsb.org")\r
+ _jmol.defaultURL_RCSB || (_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF")\r
+ fileformat || (fileformat="PDB")\r
+ pdbid || (pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel))\r
+ if(!pdbid || pdbid.length != 4)return ""\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())\r
+ fileformat=="CIF" || (url=url.replace(/CIF/,fileformat))\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thismodel=pdbid\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.thisurl=url\r
+ _jmol.modelArray = []\r
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)\r
+ _jmolDomScriptLoad(url)\r
+ return url\r
+}\r
+\r
+\r
+///////////////auto load NIH CACTVS data -- compound name or SMILES ///////////\r
+\r
+function jmolLoadAjax_STOLAF_NIH(compoundid,optionalscript,targetSuffix){\r
+ _jmol.thismodel || (_jmol.thismodel = "aspirin")\r
+ _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")\r
+ _jmol.defaultURL_NIH || (_jmol.defaultURL_NIH="http://cactus.nci.nih.gov/chemical/structure/FILE/file?format=sdf&get3d=True")\r
+ compoundid || (compoundid=prompt("Enter a compound name or a SMILES string:",_jmol.thismodel))\r
+ if(!compoundid)return ""\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ var url=_jmol.defaultURL_NIH.replace(/FILE/g,compoundid)\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thismodel=compoundid\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.thisurl=url\r
+ _jmol.modelArray = []\r
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)\r
+ _jmolDomScriptLoad(url)\r
+ return url\r
+}\r
+\r
+\r
+/////////////// St. Olaf College AJAX server -- ANY URL ///////////\r
+\r
+function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){\r
+ _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"\r
+ _jmol.thisurlANY || (_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol")\r
+ url || (url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY))\r
+ userid || (userid="0")\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.modelArray = []\r
+ _jmol.thisurl = url\r
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)\r
+ _jmolDomScriptLoad(url)\r
+}\r
+\r
+\r
+/////////////// Mineralogical Society of America (MSA) data /////////\r
+\r
+function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){\r
+\r
+ _jmol.thiskeyMSA || (_jmol.thiskeyMSA = "mineral")\r
+ _jmol.thismodelMSA || (_jmol.thismodelMSA = "quartz")\r
+ _jmol.ajaxURL_MSA || (_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs")\r
+ key || (key=prompt("Enter a field:", _jmol.thiskeyMSA))\r
+ if(!key)return ""\r
+ value || (value=prompt("Enter a "+key+":", _jmol.thismodelMSA))\r
+ if(!value)return ""\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ optionalscript == 1 && (optionalscript='load "" {1 1 1}')\r
+ var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thiskeyMSA=key\r
+ _jmol.thismodelMSA=value\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.thisurl=url\r
+ _jmol.modelArray = []\r
+ loadModel=_jmolLoadModel\r
+ _jmolDomScriptLoad(url)\r
+ return url\r
+}\r
+\r
+\r
+\r
+function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){\r
+ userid || (userid="0")\r
+ targetSuffix || (targetSuffix="0")\r
+ optionalscript || (optionalscript="")\r
+ _jmol.optionalscript=optionalscript\r
+ _jmol.thismodel=userid\r
+ _jmol.thistargetsuffix=targetSuffix\r
+ _jmol.modelArray = []\r
+ _jmol.thisurl = url\r
+ url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix\r
+ _jmolDomScriptLoad(url)\r
+}\r
+\r
+\r
+//// in case Jmol library has already been loaded:\r
+\r
+}catch(e){}\r
+\r
+///////////////moving atoms //////////////\r
+\r
+// HIGHLY experimental!!\r
+\r
+function jmolSetAtomCoord(i,x,y,z,targetSuffix){\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)\r
+}\r
+\r
+function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){\r
+ _jmolCheckBrowser();\r
+ var applet=_jmolGetApplet(targetSuffix);\r
+ if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)\r
+}\r
+\r
+\r
+///////////////applet fake for testing buttons/////////////\r
+\r
+\r
+if(_jmol.useNoApplet){\r
+ jmolApplet = function(w){\r
+ var s="<table style='background-color:black' width="+w+"><tr height="+w+">"\r
+ +"<td align=center valign=center style='background-color:white'>"\r
+ +"Applet would be here"\r
+ +"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"\r
+ +"</td></tr></table>"\r
+ return _jmolDocumentWrite(s)\r
+ }\r
+\r
+ _jmolFindApplet = function(){return jmolApplet0}\r
+\r
+ jmolApplet0 = {\r
+ script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}\r
+ ,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script} \r
+ ,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}\r
+ }\r
+}\r
+\r
+\r
+///////////////////////////////////////////\r
+\r
+ // This should no longer be needed, jmolResizeApplet() is better; kept for backwards compatibility\r
+ /*\r
+ Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%).\r
+ targetSuffix is optional and defaults to zero (first applet in page).\r
+ Both w and h are optional, but needed if you want to use targetSuffix.\r
+ h defaults to w\r
+ w defaults to 100% of window\r
+ If either w or h is between 0 and 1, then it is taken as percent/100.\r
+ If either w or h is greater than 1, then it is taken as a size (pixels). \r
+ */\r
+function jmolResize(w,h,targetSuffix) {\r
+ _jmol.alerted = true;\r
+ var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0);\r
+ var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0);\r
+ if (_jmol.browser=="msie") {\r
+ var width=document.body.clientWidth;\r
+ var height=document.body.clientHeight;\r
+ } else {\r
+ var netscapeScrollWidth=15;\r
+ var width=window.innerWidth - netscapeScrollWidth;\r
+ var height=window.innerHeight-netscapeScrollWidth;\r
+ }\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ if(!applet)return;\r
+ applet.style.width = (percentW ? width * percentW/100 : w)+"px";\r
+ applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px";\r
+ //title=width + " " + height + " " + (new Date());\r
+}\r
+\r
+// 13 Jun 09 -- makes jmolResize() obsolete (kept for backwards compatibility)\r
+function jmolResizeApplet(size,targetSuffix) {\r
+ // See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()]\r
+ // Special case: an empty value for width or height is accepted, meaning no change in that dimension.\r
+ _jmol.alerted = true;\r
+ var applet = _jmolGetApplet(targetSuffix);\r
+ if(!applet)return;\r
+ var sz = _jmolGetAppletSize(size, "px");\r
+ sz[0] && (applet.style.width = sz[0]);\r
+ sz[1] && (applet.style.height = sz[1]);\r
+}\r
+\r
+function _jmolGetAppletSize(size, units) {\r
+ /* Accepts single number or 2-value array, each one can be one of:\r
+ percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)\r
+ [width, height] array of strings is returned, with units added if specified.\r
+ Percent is relative to container div or element (which should have explicitly set size).\r
+ */\r
+ var width, height;\r
+ if ( (typeof size) == "object" && size != null ) {\r
+ width = size[0]; height = size[1];\r
+ } else {\r
+ width = height = size;\r
+ }\r
+ return [_jmolFixDim(width, units), _jmolFixDim(height, units)];\r
+}\r
+\r
+function _jmolFixDim(x, units) {\r
+ var sx = "" + x;\r
+ return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])\r
+ : sx.indexOf("%") == sx.length-1 ? sx \r
+ : (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"\r
+ : (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]\r
+ : x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]\r
+ : x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1] \r
+ : x) + (units ? units : ""));\r
+}\r
+\r
+\r
+\r
+\r
--- /dev/null
+>FER_CAPAA Ferredoxin
+ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEG
+WVLTCVAYPQSDVTIETHKEAELVG-
+>FER_CAPAN Ferredoxin, chloroplast precursor
+ASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEG
+WVLTCVAYPQSDVTIETHKEAELVG-
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor
+ASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAG
+FVLTCVAYPKGDVTIETHKEEELTA-
+>Q93XJ9_SOLTU Ferredoxin I precursor
+ASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAG
+FVLTCVAYPKCDVTIETHKEEELTA-
+>FER1_MESCR Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEG
+WVLTCVAYPTGDVTIETHKEEELTA-
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEG
+WVLTCAAYPVSDVTIETHKEEELTA-
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
+ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEG
+FVLTCAAYPTSDVTIETHKEEDIV--
+>FER2_ARATH Ferredoxin-2, chloroplast precursor
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEG
+YVLTCVAYPTSDVVIETHKEEAIM--
+>FER1_PEA Ferredoxin-1, chloroplast precursor
+ASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAG
+FVLTCVAYPTSDVVIETHKEEDLTA-
+>Q7XA98_TRIPR Ferredoxin I
+ATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGG
+WVLTCVAFPTSDVTIETHKEEELTA-
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor
+ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG
+WVLTCHAYPTSDVVIETHKEEELTGA
+>O80429_MAIZE Ferredoxin
+ATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADG
+WVLTCAAYPTSDVVIETHKEDDLL--
+>Q93Z60_ARATH At1g10960/T19D16_12
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------
+--------------------------
+>FER3_RAPSA Ferredoxin, leaf L-A
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEG
+FVLTCAAYPTSDVTIETHREEDMV--
+>FER_BRANA Ferredoxin
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEG
+FVLTCAAYPTSDVTIETHKEEELV--
--- /dev/null
+Lupas_21:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+Lupas_14:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+Lupas_28:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+
+jnetpred:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
+JNETCONF:1,3,1,2,7,7,9,9,7,1,6,8,9,8,1,3,5,5,1,6,8,9,7,4,8,8,7,2,3,2,0,2,1,2,5,7,8,8,7,6,4,2,1,3,5,7,8,7,5,4,4,5,7,5,2,5,5,1,4,2,0,1,5,6,7,7,5,4,5,4,5,6,6,3,1,1,1,4,6,1,6,9,9,9,8,8,7,0,8,9,9,7,2,8,9,9,8,
+JNETSOL25:B,-,B,-,-,B,B,B,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,B,B,-,B,-,B,-,-,-,-,-,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,B,B,-,-,-,-,-,-,B,-,-,B,B,B,B,B,B,B,B,B,B,-,-,-,-,B,B,-,-,
+JNETSOL5:-,-,-,-,-,-,-,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,B,B,B,B,-,-,-,-,-,-,-,B,-,-,
+JNETSOL0:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,
+JNETPROPH:0.44514,0.02676,0.50891,0.59931,0.03767,0.31300,0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,
+JNETPROPB:0.59931,0.03767,0.31300,0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,0.52815,0.46401,0.03979,
+JNETPROPC:0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,0.52815,0.46401,0.03979,0.40515,0.56556,0.03815,
+JNETHMM:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
+JNETALIGN:-,-,-,E,E,E,E,E,-,-,-,-,-,-,E,-,-,-,-,-,-,E,E,E,E,H,H,H,H,H,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,-,-,-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,E,E,H,H,H,-,-,-,-,
+align1;Sequence0/1.97:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,D,C,P,D,D,V,Y,I,L,D,Q,A,E,E,A,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,I,A,G,G,A,V,D,Q,T,D,G,N,F,L,D,D,D,Q,L,E,E,G,W,V,L,T,C,V,A,Y,P,Q,S,D,V,T,I,E,T,H,K,E,A,E,L,V,G,
+align2;Sequence1/1.144:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,D,C,P,D,N,V,Y,I,L,D,Q,A,E,E,A,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,I,A,G,G,A,V,D,Q,T,D,G,N,F,L,D,D,D,Q,L,E,E,G,W,V,L,T,C,V,A,Y,P,Q,S,D,V,T,I,E,T,H,K,E,A,E,L,V,G,
+align3;Sequence2/1.144:A,S,Y,K,V,K,L,I,T,P,E,G,P,I,E,F,E,C,P,D,D,V,Y,I,L,D,Q,A,E,E,E,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,A,G,S,V,D,Q,S,D,G,N,F,L,D,E,D,Q,E,A,A,G,F,V,L,T,C,V,A,Y,P,K,G,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align4;Sequence3/1.144:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,E,C,P,D,D,V,Y,I,L,D,Q,A,E,E,E,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,A,G,T,V,D,Q,S,D,G,K,F,L,D,D,D,Q,E,A,A,G,F,V,L,T,C,V,A,Y,P,K,C,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align5;Sequence4/1.149:A,S,Y,K,V,K,L,V,T,P,D,G,T,Q,E,F,E,C,P,S,D,V,Y,I,L,D,H,A,E,E,V,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,G,G,E,V,D,Q,S,D,G,S,F,L,D,D,E,Q,I,E,A,G,F,V,L,T,C,V,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,D,L,T,A,
+align6;Sequence5/1.152:A,T,Y,K,V,K,L,I,T,P,E,G,P,Q,E,F,D,C,P,D,D,V,Y,I,L,D,H,A,E,E,V,G,I,E,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,N,G,N,V,N,Q,E,D,G,S,F,L,D,D,E,Q,I,E,G,G,W,V,L,T,C,V,A,F,P,T,S,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align7;Sequence6/1.148:A,A,Y,K,V,T,L,V,T,P,E,G,K,Q,E,L,E,C,P,D,D,V,Y,I,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,S,G,S,V,N,Q,D,D,G,S,F,L,D,D,D,Q,I,K,E,G,W,V,L,T,C,V,A,Y,P,T,G,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align8;Sequence7/1.147:A,A,Y,K,V,T,L,V,T,P,T,G,N,V,E,F,Q,C,P,D,D,V,Y,I,L,D,A,A,E,E,E,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,L,K,T,G,S,L,N,Q,D,D,Q,S,F,L,D,D,D,Q,I,D,E,G,W,V,L,T,C,A,A,Y,P,V,S,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align9;Sequence8/1.96:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,D,D,D,Q,I,A,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,R,E,E,D,M,V,.,
+align10;Sequence9/1.148:A,T,Y,K,V,K,F,I,T,P,E,G,E,L,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,D,D,E,Q,I,G,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,K,E,E,D,I,V,.,
+align11;Sequence10/1.96:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,F,V,D,Q,S,D,E,S,F,L,D,D,D,Q,I,A,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,K,E,E,E,L,V,.,
+align12;Sequence11/1.148:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,E,E,D,V,Y,V,L,D,A,A,E,E,A,G,L,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,I,D,Q,S,D,Q,S,F,L,D,D,E,Q,M,S,E,G,Y,V,L,T,C,V,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,A,I,M,.,
+align13;Sequence12/1.118:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,E,E,D,V,Y,V,L,D,A,A,E,E,A,G,L,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,I,D,Q,S,D,Q,S,F,L,D,D,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,
+align14;Sequence13/1.150:A,T,Y,N,V,K,L,I,T,P,E,G,E,V,E,L,Q,V,P,D,D,V,Y,I,L,D,Q,A,E,E,D,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,Y,L,D,D,G,Q,I,A,D,G,W,V,L,T,C,H,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,E,L,T,G,
+align15;Sequence14/1.140:A,T,Y,N,V,K,L,I,T,P,E,G,E,V,E,L,Q,V,P,D,D,V,Y,I,L,D,F,A,E,E,E,G,I,D,L,P,F,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,N,D,N,Q,V,A,D,G,W,V,L,T,C,A,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,D,D,L,L,.,
+jpred:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
--- /dev/null
+>FER_CAPAA/1-97
+----------------------------------------------------------ASYKVKLITPDGPI
+EFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVT
+IETHKEAELVG-
+>FER_CAPAN/1-144
+------MASVSATMISTSFMPRKPAVTSLKPIP-NVG-EALFGLKS---ANGGKVTCMASYKVKLITPDGPI
+EFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVT
+IETHKEAELVG-
+>FER1_SOLLC/1-144
+------MASISGTMISTSFLPRKPAVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPEGPI
+EFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVT
+IETHKEEELTA-
+>Q93XJ9_SOLTU/1-144
+------MASISGTMISTSFLPRKPVVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPDGPI
+EFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVT
+IETHKEEELTA-
+>FER1_PEA/1-149
+---MATTPALYGTAVSTSFLRTQPMPMSVTTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQ
+EFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVV
+IETHKEEDLTA-
+>Q7XA98_TRIPR/1-152
+---MATTPALYGTAVSTSFMRRQPVPMSVATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQ
+EFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVT
+IETHKEEELTA-
+>FER1_MESCR/1-148
+--MAATTAALSGATMSTAFAPKT--PPMTAALPTNVG-RALFGLKS--SASRGRVTAMAAYKVTLVTPEGKQ
+ELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVT
+IETHKEEELTA-
+>FER1_SPIOL/1-147
+----MAATTTTMMGMATTFVPKPQAPPMMAALPSNTG-RSLFGLKT--GSRGGRMT-MAAYKVTLVTPTGNV
+EFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVT
+IETHKEEELTA-
+>FER3_RAPSA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
+IETHREEDMV--
+>FER1_ARATH/1-148
+----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
+IETHKEEDIV--
+>FER_BRANA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
+IETHKEEELV--
+>FER2_ARATH/1-148
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
+>Q93Z60_ARATH/1-118
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------
+------------
+>FER1_MAIZE/1-150
+MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVG---IMGRSA---SSRRRLRAQATYNVKLITPEGEV
+ELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVV
+IETHKEEELTGA
+>O80429_MAIZE/1-140
+---------MAATALSMSILRAPP-PCFSSPLRLRVAVAKPLAAPM----RRQLLRAQATYNVKLITPEGEV
+ELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVV
+IETHKEDDLL--
--- /dev/null
+HELIX d4d189
+MOD_RES 47e459
+TRANSIT 6f949b
+TURN 1d1e2d
+METAL 70686e
+SIGNAL 92c7dd
+VARIANT 60beac
+Pfam dc206a
+CONFLICT c46c6e
+STRAND 25c54c
+
+STARTGROUP uniprot
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER_CAPAA -1 8 83 Pfam
+Chloroplast FER_CAPAN -1 1 47 TRANSIT
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+Phosphothreonine FER_CAPAN -1 136 136 MOD_RES
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> FER_CAPAN -1 55 130 Pfam
+Chloroplast FER1_SOLLC -1 1 47 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> FER1_SOLLC -1 55 130 Pfam
+Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_130</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+Chloroplast FER1_PEA -1 1 52 TRANSIT
+L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT
+I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_PEA -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_138</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+Chloroplast FER1_MESCR -1 1 51 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_134</a></html> FER1_MESCR -1 59 134 Pfam
+Chloroplast FER1_SPIOL -1 1 50 TRANSIT
+STRAND FER1_SPIOL -1 52 59 STRAND
+TURN FER1_SPIOL -1 60 61 TURN
+STRAND FER1_SPIOL -1 62 69 STRAND
+TURN FER1_SPIOL -1 70 71 TURN
+HELIX FER1_SPIOL -1 74 80 HELIX
+TURN FER1_SPIOL -1 81 82 TURN
+STRAND FER1_SPIOL -1 88 92 STRAND
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+TURN FER1_SPIOL -1 96 97 TURN
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+STRAND FER1_SPIOL -1 98 104 STRAND
+TURN FER1_SPIOL -1 109 110 TURN
+HELIX FER1_SPIOL -1 116 121 HELIX
+TURN FER1_SPIOL -1 122 122 TURN
+STRAND FER1_SPIOL -1 123 125 STRAND
+HELIX FER1_SPIOL -1 126 128 HELIX
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+STRAND FER1_SPIOL -1 130 133 STRAND
+STRAND FER1_SPIOL -1 135 138 STRAND
+HELIX FER1_SPIOL -1 142 144 HELIX
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_133</a></html> FER1_SPIOL -1 58 133 Pfam
+I -> V FER3_RAPSA -1 8 8 VARIANT
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+S -> T FER3_RAPSA -1 55 55 VARIANT
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+R -> K FER3_RAPSA -1 91 91 VARIANT
+M -> V FER3_RAPSA -1 95 95 VARIANT
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER3_RAPSA -1 8 83 Pfam
+Chloroplast FER1_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_ARATH -1 60 135 Pfam
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_83</a></html> FER_BRANA -1 8 83 Pfam
+Chloroplast FER2_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER2_ARATH -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_118</a></html> Q93Z60_ARATH -1 60 118 Pfam
+Chloroplast FER1_MAIZE -1 1 52 TRANSIT
+STRAND FER1_MAIZE -1 57 59 STRAND
+STRAND FER1_MAIZE -1 72 74 STRAND
+HELIX FER1_MAIZE -1 76 80 HELIX
+TURN FER1_MAIZE -1 81 84 TURN
+STRAND FER1_MAIZE -1 90 97 STRAND
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+TURN FER1_MAIZE -1 98 99 TURN
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+TURN FER1_MAIZE -1 118 119 TURN
+HELIX FER1_MAIZE -1 120 123 HELIX
+TURN FER1_MAIZE -1 128 129 TURN
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+STRAND FER1_MAIZE -1 132 135 STRAND
+STRAND FER1_MAIZE -1 137 141 STRAND
+TURN FER1_MAIZE -1 142 142 TURN
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_135</a></html> FER1_MAIZE -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_127</a></html> O80429_MAIZE -1 52 127 Pfam
+ENDGROUP uniprot
--- /dev/null
+>FER_CAPAA Ferredoxin\r
+-----------------------------------------------------------ASYKVKLITPDGP\r
+IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV\r
+TIETHKEAELVG-\r
+>FER_CAPAN Ferredoxin, chloroplast precursor\r
+MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP\r
+IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV\r
+TIETHKEAELVG-\r
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor\r
+MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP\r
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV\r
+TIETHKEEELTA-\r
+>Q93XJ9_SOLTU Ferredoxin I precursor\r
+MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP\r
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV\r
+TIETHKEEELTA-\r
+>FER1_PEA Ferredoxin-1, chloroplast precursor\r
+MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT\r
+QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV\r
+VIETHKEEDLTA-\r
+>Q7XA98_TRIPR Ferredoxin I\r
+MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP\r
+QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV\r
+TIETHKEEELTA-\r
+>FER1_MESCR Ferredoxin-1, chloroplast precursor\r
+MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK\r
+QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV\r
+TIETHKEEELTA-\r
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor\r
+MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN\r
+VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV\r
+TIETHKEEELTA-\r
+>FER3_RAPSA Ferredoxin, leaf L-A\r
+-----------------------------------------------------------ATYKVKFITPEGE\r
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV\r
+TIETHREEDMV--\r
+>FER1_ARATH Ferredoxin-1, chloroplast precursor\r
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE\r
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV\r
+TIETHKEEDIV--\r
+>FER_BRANA Ferredoxin\r
+-----------------------------------------------------------ATYKVKFITPEGE\r
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV\r
+TIETHKEEELV--\r
+>FER2_ARATH Ferredoxin-2, chloroplast precursor\r
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE\r
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV\r
+VIETHKEEAIM--\r
+>Q93Z60_ARATH At1g10960/T19D16_12\r
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE\r
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------\r
+-------------\r
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor\r
+MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE\r
+VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV\r
+VIETHKEEELTGA\r
+>O80429_MAIZE Ferredoxin\r
+MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE\r
+VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV\r
+VIETHKEDDLL--\r
--- /dev/null
+>FER1_MAIZE/53-118 Ferredoxin-1, chloroplast precursor
+ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDD
+>FER_CAPAA/1-66 Ferredoxin
+ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDD
+>FER_CAPAN/48-113 Ferredoxin, chloroplast precursor
+ASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDD
+>FER1_SOLLC/48-113 Ferredoxin-1, chloroplast precursor
+ASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDE
+>Q93XJ9_SOLTU/48-113 Ferredoxin I precursor
+ASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDD
+>FER1_PEA/53-118 Ferredoxin-1, chloroplast precursor
+ASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDD
+>Q7XA98_TRIPR/56-121 Ferredoxin I
+ATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDD
+>FER1_MESCR/52-117 Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDD
+>FER1_SPIOL/51-116 Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDD
+>FER3_RAPSA/1-66 Ferredoxin, leaf L-A
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
+>FER1_ARATH/53-118 Ferredoxin-1, chloroplast precursor
+ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
+>FER_BRANA/1-66 Ferredoxin
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDD
+>FER2_ARATH/53-118 Ferredoxin-2, chloroplast precursor
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
+>Q93Z60_ARATH/53-118 At1g10960/T19D16_12
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
+>O80429_MAIZE/45-110 Ferredoxin
+ATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLND
--- /dev/null
+title=Applet Parameters
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+status=published
+~~~~~~
+ <p>
+ <strong>Quick Links:<ul><li>Download the applet jar file from <a
+ href="jalviewApplet.jar">here</a>
+ </li>
+ <li>Parameters are described <a href="#parameters">below</a></li>
+ <li>The javascript API is described <a
+ href="jalviewLiteJs.html">here</a></li>
+ </ul></strong>
+ </p>
+ <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+ <p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
+ <a name="parameters"></a> <table width="97%" class="borderTable" align="center" >
+ <tr>
+ <td width="103" height="23"><strong><param name=""</strong></td>
+ <td width="80" ><strong>value=""></strong></td>
+ <td width="100%"><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td>permissions</td>
+ <td>sandbox</td>
+ <td><strong>This parameter is necessary, and must have the value <em>sandbox</em> to allow the JalviewLite applet to run.</strong></td>
+ </tr>
+ <tr>
+ <td>file</td>
+ <td>fileName</td>
+ <td>The file to open, must be on same server as the applet.</td>
+ </tr>
+ <tr>
+ <td>sequence1,<br>
+ sequence2,<br>
+ sequence3</td>
+ <td>sequence in (preferably) PFAM or Fasta format</td>
+ <td>The alignment can be added as a series of sequences instead of
+ from a file.</td>
+ </tr>
+ <tr>
+ <td>tree</td>
+ <td>fileName</td>
+ <td>Tree file in Newick format</td>
+ </tr>
+ <tr>
+ <td>features</td>
+ <td>fileName</td>
+ <td>Jalview Features file to be applied to the alignment</td>
+ </tr>
+ <tr>
+ <td>annotations</td>
+ <td>fileName</td>
+ <td>Jalview Annotation file will be added to the alignment</td>
+ </tr>
+ <tr>
+ <td>jnetfile</td>
+ <td>fileName</td>
+ <td>Secondary structure predictions from a <a
+ href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise
+ file will be added to the first sequence in the alignment.</td>
+ </tr>
+ <tr>
+ <td>PDBfile(x)</td>
+ <td><p>fileName seq1 seq2 seq3</p>
+ <p>or</p>
+ <p>fileName A=seq1 B=seq2 C=seq3</p></td>
+ <td>PDB file which is to be associated with a sequence, followed by
+ space separated list of alignment sequence ids. PDB chains can be
+ specifed to map to particular sequence by using A=SeqA notation</td>
+ </tr>
+ <tr>
+ <td><p>PDBSeq<br>
+ *Not needed post Jalview 2.3, use PDBFile instead</p></td>
+ <td>SequenceId</td>
+ <td>The sequence to associate a PDB file with. Note the value is case
+ sensitive.</td>
+ </tr>
+ <tr>
+ <td>defaultColour</td>
+ <td> <em>One of: </em><br>
+ Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+ <td>Default is no colour.</td>
+ </tr>
+ <tr>
+ <td>userDefinedColour</td>
+ <td><p><em>Example:</em><br>
+ D,E=red; K,R,H=0022FF; c=yellow</p></td>
+ <td>Define residue colours</td>
+ </tr>
+ <tr>
+ <td height="35">showFullId</td>
+ <td>true <em>or</em> false</td>
+ <td>if true displays start and end residue at the end of sequence
+ Id.</td>
+ </tr>
+ <tr>
+ <td>showAnnotation</td>
+ <td>true <em>or</em> false</td>
+ <td>If true shows the annotation panel below the alignment.</td>
+ </tr>
+ <tr>
+ <td>showConservation</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>showQuality</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>showConsensus</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>sortBy</td>
+ <td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
+ <td> Sorts the alignment on startup</td>
+ </tr>
+ <tr>
+ <td>RGB</td>
+ <td>colour as hex string</td>
+ <td>Background colour for applet button - purely cosmetic to blend
+ in with your web page. For orange, enter the value FF6600</td>
+ </tr>
+ <tr>
+ <td>embedded</td>
+ <td>true <em>or</em> false</td>
+ <td>The applet is embedded in the web page, the "Start Jalview"
+ button is not displayed.</td>
+ </tr>
+ <tr>
+ <td>windowWidth</td>
+ <td>value</td>
+ <td>frame width</td>
+ </tr>
+ <tr>
+ <td>windowHeight</td>
+ <td>value</td>
+ <td>frame height</td>
+ </tr>
+ <tr>
+ <td>label</td>
+ <td>label text</td>
+ <td>Change text for the Launch Jalview Button</td>
+ </tr>
+ <tr>
+ <td>wrap</td>
+ <td>true <em>or</em> false</td>
+ <td>Opens new windows in wrapped mode</td>
+ </tr>
+ <tr>
+ <td>linkLabel_1</td>
+ <td>EMBL-EBI Search</td>
+ <td rowspan="2"><p>Right click on sequence id to see list of available
+ links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
+ value. For multiple links, increment the label and url name by
+ 1. ie <br>
+ <param name="linkLabel_2" ..., <br>
+ <param name="linkUrl_2"....<br>
+ </p>
+ <p>Regular expressions may also be used (<em>since Jalview 2.4</em>) to process the ID string inserted into the URL:
+ <br>$SEQUENCE_ID=/<regex to extract ID>/=$<br><em>Use the debug flag to check parsing and make sure that special symbols are properly escaped (particularly when generating applet tags from CGI scripts).
+ <br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
+ </tr>
+ <tr>
+ <td> <p>
+ <br>
+ linkUrl_1<br>
+ </p></td>
+ <td><p><br>
+ http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
+ </td>
+ </tr>
+ <tr>
+ <td>showFeatureSettings</td>
+ <td>true <em>or</em> false</td>
+ <td>Shows the feature settings window when starting the applet</td>
+ </tr>
+ <tr>
+ <td>showfeaturegroups</td>
+ <td><em>separator</em> separated list of feature groups</td>
+ <td>Display the features in the given groups on the alignment</td>
+ </tr>
+ <tr>
+ <td>hidefeaturegroups</td>
+ <td><em>separator</em> separated list of feature groups</td>
+ <td>Hide the features in the given groups on the alignment
+ (will be overridden by showfeaturegroups for group names
+ found in both lists)</td>
+ </tr>
+ <tr>
+ <td>application_url</td>
+ <td><p><em>URL of dynamic JNLP servlet,</em></p>
+ <p>http://www.jalview.org/services/launchApp</p></td>
+ <td>Launches full application with original alignment, features and
+ annotations files used in applet</td>
+ </tr>
+ <tr>
+ <td>separator</td>
+ <td><em>non-empty separator string</em><br>default: |</td>
+ <td>string used to separate fields in list parameters (such as <em>showfeaturegroups</em>)</td>
+ </tr>
+ <tr><td>debug</td>
+ <td>true</td>
+ <td>Instruct the applet to output additional debug messages to the java console</td>
+ </tr>
+ <tr><td>nojmol</td>
+ <td>false</td>
+ <td>When set, do not try to find Jmol classes. Set this to supress URL not found errors appearing
+ in server logs when Jmol is not available.
+ </td>
+ </tr>
+ <tr><td>showbutton</td>
+ <td>true</td>
+ <td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
+ </tr>
+ </tr>
+ <tr><td>sortByTree</td>
+ <td>true or false (default is false)</td>
+ <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>
+ </tr>
+ <tr>
+ <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>
+ </tr>
+ <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>
+ <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>
+ </tr>
+ <tr><td>heightScale</td>
+ <td>1.0 or greater</td>
+ <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (<em>since 2.5.1</em>)</td>
+ </tr>
+ <tr><td>widthScale</td>
+ <td>1.0 or greater</td>
+ <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
+ </tr>
+ <tr><td>centrecolumnlabels</td>
+ <td>true of false (default is false)</td>
+ <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
+ <tr><td>showUnconserved</td>
+ <td>true of false (default is false)</td>
+ <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
+ </tr>
+ <tr><td>upperCase</td>
+ <td><em>bold</em> or other value</td>
+ <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
+ </tr>
+ <tr><td>automaticScrolling</td>
+ <td>true of false (default is true)</td>
+ <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
+ </tr>
+
+ <tr><td>showGroupConsensus</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
+ </tr>
+
+ <tr><td>showGroupConservation</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>showConsensusHistogram</td>
+ <td>true of false (default is true)</td>
+ <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>showSequenceLogo</td>
+ <td>true of false (default is false)</td>
+ <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>normaliseSequenceLogo</td>
+ <td>true of false (default is false)</td>
+ <td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.8</em>)</td>
+ </tr>
+ <tr><td>oninit</td>
+ <td><em>after_init()</em></td>
+ <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>relaxedidmatch</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>alignpdbfiles</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>externalstructureviewer</td>
+ <td><em>true or false (default is false)</em></td>
+ <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>
+
+ </tr>
+ <tr><td>annotationcolour_max</td>
+ <td>colour name or RGB hex triplet (default is red)</td>
+ <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>annotationcolour_min</td>
+ <td>colour name or RGB hex triplet (default is orange)</td>
+ <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>jalviewhelpurl</td>
+ <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
+ <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>resolvetocodebase</td>
+ <td>True or False (False)</td>
+ <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>
+ </tr>
+ <tr><td>scoreFile</td>
+ <td>file</td>
+ <td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
+ </tr>
+ </table>
+ <p><h2><a name="appletdeploymentnotes"/>Notes on applet deployment</h2><br/>
+ <ul>
+ <li>Package all your data files into a single (or multiple) zip / jar
+ files. This is very useful to reduce download time of large data files.
+ The applet archive tag can take multiple entries separated by commas,
+ eg<br>
+ <pre><applet code="jalview.bin.JalviewLite"<em><strong>
+ archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
+ </pre></li>
+ <li> Use Jalview for input to a HTML form. For an example of how to
+ code this using Javascript, click <a href="formComplete.html">here</a>.
+ <br>
+ </li>
+ <li>Embed Jalview into the web page, without the "Start Jalview"
+ button by setting the embed parameter to true;<br>
+ <param name="embedded"
+ value="true"> </li>
+ </ul>
+ <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
+ <ul>
+ <li>Normalised sequence logo display
+ </li>
+ <li>RNA secondary structure annotation row
+ </li>
+<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></li>
+<li>To use Jmol as the structure viewer for Jalview, you must include
+ the jar file in the applet archive argument thus:<br>
+ <pre>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre>
+ </li>
+ <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
+ Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
+ original Jalview structure viewer will still be available. <br>
+ </li>
+
+ </ul>
+ <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
+ <ul>
+ <li>Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
+ <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul>
+ </li>
+ <li>New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
+ </li></ul>
+ <p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
+ <ul>
+ <li>Jmol compatibility updated to Jmol 12.1.x series</li>
+ <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
+ the Jmol binary distribution available at the Jmol Sourceforge site,
+ or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
+ <li>Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</li>
+ </ul>
+ <br><strong>**NEW FEATURES** in Jalview 2.5</strong></p>
+ <ul>
+ <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li>
+ </ul>
+ <br><strong>**NEW FEATURES** in Jalview 2.4</strong></p>
+ <ul>
+ <li>New applet API methods for feature display control, views, and obtaining current selection via javascript.</li>
+ <li>Group show and hide parameters:
+ "showfeaturegroups" and
+ "hidefeaturegroups". Both take a list
+ of feature group names (separarated by "|" by default) to hide or show on the displayed
+ alignment.
+ </li>
+ <li>Regular expressions can be used in URL links for sequence IDs.</li>
+ <li>"debug" parameter to control verbosity of the applet's console output.</li>
+ <li>"showbutton" parameter to disable launch button and open JalviewLite immediatly.</li>
+ <li>"nojmol" parameter to disable check for Jmol classes.</li>
+ </ul><br>
+ <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
+ <ul>
+ <li>Note that Parameter "PDBFile" now takes
+ the PDB file followed by a space separated list of alignment sequence
+ ids to associate the structure to. It is also possible to associate
+ multiple PDB files by adding an incremental value to PDBFile (up to
+ 10). It is also possible to map specific sequences to specific chains
+ by using the following notation:<br>
+ <br>
+ <pre>
+ <param name="PDBFile" value="First.pdb SeqA SeqB
+ SeqC"><br>
+ <param name="PDBFile2" value="Second.pdb
+ A=SeqA B=SeqB C=SeqC"><br>
+ <param name="PDBFile3" value="Third.pdb
+ D=SeqX B=SeqY C=SeqZ"><br>
+ </pre>
+ </li>
+ <li>Note parameter "PDBSeq" is no longer required.<br>
+ </li>
+ <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li>
+ <p> </p>
+ </li>
+ </ul>
+ <strong>**NEW FEATURES** in Jalview 2.1</strong>
+ <ul>
+ <li>Jalview Applet can read and display JNet secondary structure annotation
+ directly via the <strong>jnetfile</strong> parameter. <br>
+ </li>
+ <li>Param "UserDefinedColour" - specify your own colours for each residue using a semi colon
+ separated list. Multiple residues can be assigned the same colour
+ using commas. eg:<br>
+ <pre><param name="userDefinedColour"
+ value="D,E=red; K,R,H=0022FF; C=yellow"></pre>
+ </li>
+ <li>Param "showFeatureSettings"
+ - this will display the feature settings window when the applet starts.
+ </li>
+ <li>Param "Application_URL" value="http://www.jalview.org/services/launchApp"<br/>
+ This calls a servlet which creates a JNLP file with the alignment
+ file, annotations file and features file of the applet as arguments.
+ If the user has Java installed, the returned JNLP file should start
+ up the full Jalview Application. BUT this does not currently work
+ for alignment files added to the applet in a zip file.
+ <br/>Look at the XML comments in the file downloaded from <a href="http://www.jalview.org/services/launchApp">The LaunchApp page</a> for full documentation.
+ </li>
+ <li>Alignment file can be a series of parameters using eg PFAM format
+ <br>
+ <pre><param name="sequence1"
+ value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
+ <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
+ </pre>(All the usual Jalview File formats are valid, however each
+ new line in an alignment file must be entered as a parameter)</li>
+ </ul>
+
--- /dev/null
+title=JalviewLite Examples
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+status=published
+level=0
+class=jvl_examples.ftl
+~~~~~~
+
--- /dev/null
+title=Embedded Alignment
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_embedded.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+title=Jalview and Jmol
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_embeddedWJmol.ftl
+hclass=jvl_embeddedWJmol_hdr.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+title=Access from Javascript
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_formComplete.ftl
+status=published
+level=2
+~~~~~~
+<!-- end of -->
--- /dev/null
+title=Javascript Launch
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_javascriptLaunch.ftl
+status=published
+level=2
+~~~~~~
+
--- /dev/null
+title=Linked JalviewLite applets
+type=page
+jvl=jalviewApplet.jar
+jmol=JmolApplet-12.2.4.jar
+class=jvl_linkedapplets_ng.ftl
+status=published
+level=2
+~~~~~~
--- /dev/null
+site.host=http://www.jalview.org/examples/
+render.tags=true
\ No newline at end of file
--- /dev/null
+site.host=http://www.jalview.org/
+render.tags=false
\ No newline at end of file
--- /dev/null
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ -->
+<head>
+ <TITLE>${content.title}</TITLE>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+ <![endif]-->
+
+ <!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+ <![endif]-->
+
+ <!-- dd menu -->
+ <script type="text/javascript">
+ <!--
+ var timeout = 500;
+ var closetimer = 0;
+ var ddmenuitem = 0;
+
+ // open hidden layer
+ function mopen(id)
+ {
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+ }
+ // close showed layer
+ function mclose()
+ {
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+ }
+
+ // go close timer
+ function mclosetime()
+ {
+ closetimer = window.setTimeout(mclose, timeout);
+ }
+
+ // cancel close timer
+ function mcancelclosetime()
+ {
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+ }
+
+ // close layer when click-out
+ document.onclick = mclose;
+ // -->
+ </script>
+ <script>
+ <!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+ </script>
+<#if (content.hclass?exists) >
+ <#include content.hclass />
+</#if>
+
+</head>
+
+
+<body>
+
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
--- /dev/null
+
+<h1>Embedded viewing of Alignments</h1>
+<p>The alignment below was generated from the following files:
+ <ul>
+ <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
+ FASTA format</li>
+ <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
+ Format Sequence Features file</li>
+ <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
+ Jalview Alignment Annotations File</li>
+ </ul>
+ <@jvlitebutton appjar="${content.jvl}" width=756 height=560
+ params={
+ "file":"plantfdx.fa",
+ "annotations":"plantfdx.annotations",
+ "features":"plantfdx.features",
+ "embedded":"true",
+ "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF",
+ "showFullId":"false"}></@jvlitebutton>
+ </p>
--- /dev/null
+
+ <center>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+</script>
+ <script>
+ deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
+ </script>
+ </center>
+</div>
--- /dev/null
+<script src="javascript/deployJava.js"></script>
+<script src="jmol/Jmol.js"></script>
+<script src="javascript/jquery-1.4.4.min.js"></script>
+<script src="javascript/jquery.timer.js"></script>
+<script src="javascript/jquery.blockUI.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
+<!-- <script src="archive-min.js" language="javascript"></script>
+-->
+<script src="javascript/jalview.js" language="javascript"></script>
+<script language="JavaScript">
+// instead of this, we use a custom JmolApplet spec
+// jmolInitialize('jmol');
+jmolInitialize("","JmolApplet-12.2.4.jar");
+function genHref()
+{
+ var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
+ for(i=0; i<11; i++)
+ { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
+ }
+ window.location=href;
+}
+</script>
+<script>
+ var loglevel=1;
+ function dbg(lvl,string) {
+ if (_console && lvl<=loglevel) {_console.value += string + "\n";}
+ }
+ var _lastTime=new Date();
+ var _path;
+ var _datazip;
+ var _zip;
+ var alignA;
+ var alignB;
+ var featuresA;
+ var featuresB;
+ var pairs;
+ var atompairs;
+ var structdata;
+ var jmolview;
+ var jvstructassoc;
+ var modeltofiles = new Array();
+
+ function lJvA() {
+ jvfollower = document.getElementById("jvA");
+ setConsole(document.getElementById("stdout"));
+
+ sep = jvfollower.getSeparator();
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
+
+ var _jvA=new Object();
+ _jvA.attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar',
+ width : '500',
+ height : '350',
+ mayscript : 'True',
+ scriptable: 'True',
+ id : 'jvA'
+ };
+ _jvA.parameters = {
+ java_arguments : "-Xmx256m",
+ externalstructureviewer : "true",
+ oninit : "lJvA",
+ automaticScrolling : "true",
+// <!-- defaultColour : "Strand Propensity", -->
+ file : "uniref50_mz.fa",
+
+ relaxedidmatch : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "false",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",
+ PDBfile : "1gaq.txt FER1_MAIZE",
+ permissions : "all-permissions"
+ };
+ jmolSetCallback("hoverCallback","_jmolhover");
+ jmolSetCallback("pickCallback","_jmolpick");
+ modeltofiles+="1gaq.txt";
+</script>
--- /dev/null
+
+<p align="left">
+ Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
+ href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+<div align="center">
+ <p>
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center">
+ <@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa"
+ , "treeFile":"ferredoxin.nw"
+ , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF"
+ , "showFullId":"false"
+ , "sortByTree":"True"
+ , "showSequenceLogo":"true"
+ , "showGroupConsensus":"true"} prots=true /></td>
+ <td valign="center">User Defined Colours, loads an associated
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions",
+ "file":"uniref50.fa"
+ , "features":"exampleFeatures.txt"
+ , "showFeatureSettings":"true"
+ , "wrap":"true"
+ , "showAnnotation":"false"
+ , "windowHeight":"500"
+ , "windowWidth":"650"
+ , "showFullId":"false"}/></td>
+ <td valign="center">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions"
+ , "file":"uniref50.fa"
+ , "defaultColour":"Strand Propensity"
+ , "wrap":"true"
+ , "showAnnotation":"false"
+ , "windowHeight":"500"
+ , "windowWidth":"650"
+ , "showFullId":"false"
+ , "PDBfile":"1gaq.txt FER1_MAIZE"} /></td>
+ <td valign="center">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+ , "file":"jpred_msa.fasta"
+ , "jnetfile":"jpred_msa.seq.concise"
+ , "defaultColour":"Clustal"
+ , "showAnnotation":"true"
+ , "windowHeight":"515"
+ , "windowWidth":"650"
+ , "showConservation":"false"
+ , "showQuality":"false"
+ , "showConsensus":"false"
+ , "showFullId":"false"} />
+ </td>
+ <td valign="middle">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions"
+ , "file":"RF00031_folded.stk"
+ , "defaultColour":"Purine/Pyrimidine"
+ , "showAnnotation":"true"
+ , "windowHeight":"515"
+ , "windowWidth":"650"
+ , "showConservation":"false"
+ , "showQuality":"false"
+ , "showConsensus":"true"
+ , "showFullId":"false"} prots=false /></td>
+ <td valign="center">Displays an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+</div>
\ No newline at end of file
--- /dev/null
+<strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br/></strong>
+Click the Javascript buttons below to interact with the Applet
+instance on the page.<br/>
+View the source in your browser to see how it has been done. <br/>
+<a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
+<applet code="jalview.bin.JalviewLite" width="0" height="0"
+ archive="${content.jvl}" name="Jalview">
+ <#if content.permissions?exists><param name="permissions" value="${content.permissions}"/></#if>
+ <param name="file" value="plantfdx.fa"/>
+ <param name="features" value="plantfdx.features"/>
+ <param name="wrap" value="true"/>
+ <param name="showAnnotation" value="false"/>
+ <param name="windowHeight" value="500"/>
+ <param name="windowWidth" value="650"/>
+ <param name="showFullId" value="false"/>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"/>
+ <param name="hidefeaturegroups" value="uniprot" />
+ <param name="showbutton" value="false" />
+</applet>
+<form name="exampleForm"><br/>
+ <br/>
+ <center><strong>Using the Jalview Applet for Input
+ to an HTML Form</strong></center>
+ <div align="center"><input type="button"
+ onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
+ value="Fill Form from Jalview" /> <br/>
+ <br/>
+ <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
+</form>
+<center><strong>Make a new View and Get and Set
+ Group Display List</strong></center>
+<form name="groupForm">
+ <div align="center"><input type="button"
+ onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
+ value="Get groups" /> <input type="button"
+ onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
+ <textarea name="groups" cols="55" rows="9"></textarea> <br/>
+ <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
+ value="Display groups" /> <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
+ value="Hide groups" /></div>
+</form>
+</div>
--- /dev/null
+ <SCRIPT type="text/javascript">
+ /* <![CDATA[ // */
+// From http://snipplr.com/view.php?codeview&id=1272
+//----------------------------------------
+//Wrapper function for constructing a request object.
+// Parameters:
+// reqType: The HTTP request type, such as GET or POST.
+// url: The URL of the server program.
+// asynch: Whether to send the request asynchronously or not.
+//----------------------------------------
+
+function httpRequest(reqType,url,asynch,respHandle) {
+
+ // Mozilla-based browsers
+ if (window.XMLHttpRequest) {
+ request = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ request = new ActiveXObject("Msxml2.XMLHTTP");
+ if (!request) {
+ request = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ }
+
+ // Request could still be null if neither ActiveXObject
+ // initialization succeeded
+ if (request) {
+ // If the reqType param is POST, then the fifth arg is the POSTed data
+ if (reqType.toLowerCase() != "post") {
+ initReq(reqType, url, asynch, respHandle);
+ } else {
+ // The POSTed data
+ var args = arguments[5];
+ if (args != null && args.length > 0) {
+ initReq(reqType, url, asynch, respHandle, args);
+ }
+ }
+ } else {
+ alert("Your browser does not permit the use of all " +
+ "of this application's features!");
+ }
+
+}
+
+//----------------------------------------
+//Initialize a request object that is already constructed
+//----------------------------------------
+
+function initReq(reqType, url, bool, respHandle) {
+ try {
+ // Specify the function that will handle the HTTP response
+ request.onreadystatechange = respHandle;
+ request.open(reqType, url, bool);
+ // If the reqType param is POST, then the
+ // fifth argument to the function is the POSTed data
+ if (reqType.toLowerCase() == "post") {
+ // Set the Content-Type header for a POST request
+ request.setRequestHeader("Content-Type", "application/x-ww-form-urlencoded; charset=UTF-8");
+ request.send(arguments[4]);
+ } else {
+ request.send(null);
+ }
+ } catch (errv) {
+ alert("The application cannot contact the server at the moment. " +
+ "Please try again in a few seconds.\n" +
+ "Error detail: " + errv.message);
+ }
+}
+
+// jalview launching with fetched data
+
+function startJalview(aligURL,title,alwvar) {
+ var aligment = "";
+ httpRequest("get",aligURL,true,function() {
+ if (request.readyState == 4) {
+ alignment = request.responseText;
+ eval("var "+alwvar+" = document.JalviewLite.loadAlignment(alignment,title)");
+ }
+ })
+
+}
+
+/* ]]> */
+</SCRIPT>
+ <form name="Form1">
+<applet name="JalviewLite" code="jalview.bin.JalviewLite"
+archive="${content.jvl}" width="0" height="0">
+<param name="debug" value="true"/>
+<param name="showbutton" value="false"/>
+<#if (content.permissions?exists)>
+<param name="permissions" value="${content.permissions}"/>
+</#if>
+</applet>
+
+
+ <input type="button" name="Button1" value="Start"
+onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
+ </form>
--- /dev/null
+<script src="http://www.java.com/js/deployJava.js"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script> //deployJava.debug="true";
+
+ function lJvApp() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ setConsole(document.getElementById("stdout"));
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvapp);
+ };
+
+ function lJvFollow() {
+ var jvapp = document.getElementById("jvapp");
+ var jvfollower = document.getElementById("jvfollower");
+ //jvfollower.setSeparator(""+jvfollower.getSeparator());
+ linkJvJmol(jvfollower);
+ };
+</script>
+ <strong>JalviewLite Linked Applets Demo<br></strong>
+ <p>The two applets below use <a href="JalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
+ </p>
+ <script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : 'jvapp'
+ };
+ var parameters = {
+ oninit : "lJvApp",
+ automaticScrolling : "true",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'all-permissions',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+
+ deployJava.runApplet(attributes, parameters, '1.6+');
+</script>
+<script>
+ var attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'jalviewApplet.jar',
+ width : 800,
+ height : 300,
+ mayscript : 'True', scriptable: 'True',
+ id : "jvfollower"
+ };
+ var parameters = {
+ oninit : "lJvFollow",
+ file : "plantfdx.fa",
+ annotations : "plantfdx.annotations",
+ automaticScrolling : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "true",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ linkLabel_1 : "EMBL-EBI Search",
+ linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
+ ,
+ linkLabel_2 : "Uniprot"
+ ,
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ permissions : 'all-permissions',
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ };
+ deployJava.runApplet(attributes, parameters, '1.6+');
+</script>
+ <p>
+<!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
+ <br>
+ --><form name="console" id="console"><textarea name="output"
+ id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
+ <br>
+</p>
--- /dev/null
+<#assign appparams = [ "file","features","treeFile","userDefinedColour","sortByTree","showSequenceLogo","showGroupConsensus","showFullId","linkLabel_1","linkUrl_1","linkUrl_2","linkLabel_2","windowHeight","windowWidth","showFeatureSettings","wrap","showAnnotation","defaultColour","embedded", "debug" ] />
+
+
+<#macro jvlitebutton appjar params prots=true width=140 height=35>
+<applet
+ code="jalview.bin.JalviewLite" width="${width}" height="${width}"
+ archive="${appjar}">
+<#list appparams as p><#if (params[p])?has_content><param name="${p}" value="${params[p]}"/></#if></#list>
+<#if (prots)>
+ <param name="linkLabel_1" value="Uniprot"/>
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+</#if>
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</#macro>
--- /dev/null
+
+ <!-- Fixed navbar -->
+ <div class="navbar navbar-fixed-top">
+ <div class="navbar-inner">
+ <div class="container">
+ <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="brand" href="/">JBake</a>
+ <div class="nav-collapse collapse">
+ <ul class="nav">
+ <li><a href="/index.html">Home</a></li>
+ <li><a href="about.html">About</a></li>
+ <li><a href="${config.feed_file}">Subscribe</a></li>
+ <li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <b class="caret"></b></a>
+ <ul class="dropdown-menu">
+ <li><a href="#">Action</a></li>
+ <li><a href="#">Another action</a></li>
+ <li><a href="#">Something else here</a></li>
+ <li class="divider"></li>
+ <li class="nav-header">Nav header</li>
+ <li><a href="#">Separated link</a></li>
+ <li><a href="#">One more separated link</a></li>
+ </ul>
+ </li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div>
+ </div>
+ </div>
+ <div class="container">
\ No newline at end of file
--- /dev/null
+<#include "header.ftl"/>
+<#include "macros.ftl"/>
+<#include "sidebar.ftl"/>
+<div id="content" class="content">
+
+<#if (content.class?exists) >
+ <#include content.class />
+</#if>
+<!-- content start -->
+${content.body}
+<!-- content end -->
+</div>
+<#include "footer.ftl"/>
\ No newline at end of file
--- /dev/null
+<#include "header.ftl">
+
+ <#include "menu.ftl">
+
+ <div class="page-header">
+ <h1>${content.title}</h1>
+ </div>
+
+ <p><em>${content.date?string("dd MMMM yyyy")}</em></p>
+
+ <p>${content.body}</p>
+
+ <hr>
+
+<#include "footer.ftl">
\ No newline at end of file
--- /dev/null
+<div id="sideNav">
+ <ul>
+ <#list pages as page>
+ <#assign noclass=""/>
+ <#if page.title==content.title>
+ <#assign noclass="class=\"jvlite-nav-title\"">
+ </#if>
+ <#if (((page.level!"1")?number)<1) >
+ <li ${noclass}><a href="${page.uri?substring(1)}">${page.title}</a>
+ </#if>
+ </#list>
+ <ul>
+ <#list pages as page>
+ <#assign noclass=""/>
+ <#if page.title==content.title>
+ <#assign noclass="class=\"jvlite-nav-small\"">
+ </#if>
+ <#if (((page.level!"1")?number)>0) >
+ <li ${noclass}><a href="${page.uri?substring(1)}">${page.title}</a></li>
+ </#if>
+ </#list>
+ </ul>
+ </ul>
+</div>
+
git://source.jalview.org / jalview.git / commitdiff
