From 6fa12685f5a274baad0f65db6241de29b7e5dbbf Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 19 May 2011 15:24:03 +0100 Subject: [PATCH] example applet and desktop application files that should be published to website at www.jalview.org/examples (JAL-815) base version is 2.6.1 release of Jalview --- examples/1gaq.txt | 691 ++++++++++++++++++++++++++++++++++++++++ examples/appletParameters.html | 294 +++++++++++++++++ examples/applets.html | 137 ++++++++ examples/exampleFeatures.txt | 311 ++++++++++++++++++ examples/exampleFile.jar | Bin 0 -> 2674 bytes examples/exampleFile_2_3.jar | Bin 0 -> 78764 bytes examples/ferredoxin.nw | 1 + examples/formComplete.html | 304 ++++++++++++++++++ examples/globins.jar | Bin 0 -> 3470 bytes examples/jpred_msa.fasta | 45 +++ examples/jpred_msa.seq.concise | 30 ++ examples/plantfdx.fa | 60 ++++ examples/plantfdx.features | 118 +++++++ examples/uniref50.fa | 60 ++++ 14 files changed, 2051 insertions(+) create mode 100755 examples/1gaq.txt create mode 100644 examples/appletParameters.html create mode 100755 examples/applets.html create mode 100755 examples/exampleFeatures.txt create mode 100755 examples/exampleFile.jar create mode 100644 examples/exampleFile_2_3.jar create mode 100755 examples/ferredoxin.nw create mode 100644 examples/formComplete.html create mode 100755 examples/globins.jar create mode 100755 examples/jpred_msa.fasta create mode 100755 examples/jpred_msa.seq.concise create mode 100644 examples/plantfdx.fa create mode 100644 examples/plantfdx.features create mode 100755 examples/uniref50.fa diff --git a/examples/1gaq.txt b/examples/1gaq.txt new file mode 100755 index 0000000..69d17a5 --- /dev/null +++ b/examples/1gaq.txt @@ -0,0 +1,691 @@ +HEADER OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ +ATOM 2 CA GLU A 19 20.491 30.713 36.290 1.00 74.29 C +ATOM 11 CA SER A 20 24.056 29.774 37.264 1.00 72.09 C +ATOM 17 CA LYS A 21 27.517 31.289 37.563 1.00 70.09 C +ATOM 26 CA LYS A 22 28.794 27.865 36.481 1.00 68.64 C +ATOM 35 CA GLN A 23 29.484 26.806 32.884 1.00 70.46 C +ATOM 44 CA GLU A 24 26.420 25.175 31.360 1.00 72.08 C +ATOM 53 CA GLU A 25 26.736 26.049 27.683 1.00 70.43 C +ATOM 62 CA GLY A 26 28.299 22.912 26.233 1.00 63.14 C +ATOM 66 CA VAL A 27 26.863 20.704 28.982 1.00 54.50 C +ATOM 73 CA VAL A 28 25.030 17.390 28.655 1.00 48.32 C +ATOM 80 CA THR A 29 23.728 14.677 30.991 1.00 44.86 C +ATOM 87 CA ASN A 30 22.327 11.164 30.703 1.00 45.42 C +ATOM 95 CA LEU A 31 23.332 10.459 27.102 1.00 45.42 C +ATOM 103 CA TYR A 32 23.549 6.898 28.380 1.00 45.88 C +ATOM 115 CA LYS A 33 21.656 5.321 31.262 1.00 47.27 C +ATOM 124 CA PRO A 34 21.991 2.046 33.248 1.00 48.99 C +ATOM 131 CA LYS A 35 19.339 0.560 30.970 1.00 52.75 C +ATOM 140 CA GLU A 36 21.580 0.855 27.886 1.00 53.33 C +ATOM 149 CA PRO A 37 25.154 2.015 28.678 1.00 47.54 C +ATOM 156 CA TYR A 38 27.929 2.872 26.249 1.00 41.98 C +ATOM 168 CA VAL A 39 30.355 -0.017 25.909 1.00 41.48 C +ATOM 175 CA GLY A 40 33.823 1.485 25.966 1.00 37.59 C +ATOM 179 CA ARG A 41 37.165 -0.277 26.122 1.00 39.77 C +ATOM 190 CA CYS A 42 40.148 -0.029 28.442 1.00 36.51 C +ATOM 196 CA LEU A 43 43.095 1.441 26.554 1.00 36.13 C +ATOM 204 CA LEU A 44 45.231 2.023 29.649 1.00 33.55 C +ATOM 212 CA ASN A 45 45.140 1.026 33.307 1.00 27.79 C +ATOM 220 CA THR A 46 48.056 1.800 35.617 1.00 28.75 C +ATOM 227 CA LYS A 47 48.542 1.776 39.388 1.00 30.31 C +ATOM 236 CA ILE A 48 49.564 5.317 40.376 1.00 31.32 C +ATOM 244 CA THR A 49 50.339 4.682 44.059 1.00 37.62 C +ATOM 251 CA GLY A 50 53.585 3.317 45.460 1.00 44.49 C +ATOM 255 CA ASP A 51 53.706 -0.448 46.087 1.00 52.89 C +ATOM 263 CA ASP A 52 53.910 0.545 49.751 1.00 55.23 C +ATOM 271 CA ALA A 53 50.816 2.767 50.056 1.00 53.34 C +ATOM 276 CA PRO A 54 47.904 1.940 52.405 1.00 50.60 C +ATOM 283 CA GLY A 55 45.420 1.579 49.561 1.00 50.35 C +ATOM 287 CA GLU A 56 46.098 1.286 45.836 1.00 42.53 C +ATOM 296 CA THR A 57 44.534 3.816 43.480 1.00 41.14 C +ATOM 303 CA TRP A 58 44.540 3.423 39.708 1.00 35.60 C +ATOM 317 CA HIS A 59 44.468 5.853 36.796 1.00 31.89 C +ATOM 327 CA MET A 60 42.658 4.227 33.866 1.00 31.65 C +ATOM 335 CA VAL A 61 41.716 5.345 30.350 1.00 30.43 C +ATOM 342 CA PHE A 62 38.669 4.172 28.360 1.00 34.36 C +ATOM 353 CA SER A 63 37.657 4.908 24.772 1.00 34.69 C +ATOM 359 CA THR A 64 34.448 6.828 23.951 1.00 36.96 C +ATOM 366 CA GLU A 65 34.691 7.644 20.254 1.00 40.08 C +ATOM 375 CA GLY A 66 33.742 11.183 21.285 1.00 40.22 C +ATOM 379 CA LYS A 67 30.272 9.763 22.003 1.00 41.93 C +ATOM 388 CA ILE A 68 30.279 11.116 25.577 1.00 41.52 C +ATOM 396 CA PRO A 69 30.791 14.926 25.537 1.00 42.35 C +ATOM 403 CA TYR A 70 31.228 15.232 29.299 1.00 39.84 C +ATOM 415 CA ARG A 71 32.639 18.451 30.768 1.00 44.14 C +ATOM 426 CA GLU A 72 35.122 19.278 33.515 1.00 43.82 C +ATOM 435 CA GLY A 73 33.472 18.458 36.835 1.00 41.97 C +ATOM 439 CA GLN A 74 30.929 15.874 35.657 1.00 37.19 C +ATOM 448 CA SER A 75 31.285 12.124 36.138 1.00 38.28 C +ATOM 454 CA ILE A 76 30.458 8.792 34.539 1.00 36.84 C +ATOM 462 CA GLY A 77 28.983 5.620 35.918 1.00 35.39 C +ATOM 466 CA VAL A 78 30.311 2.108 35.530 1.00 32.05 C +ATOM 473 CA ILE A 79 28.458 -1.201 35.591 1.00 32.67 C +ATOM 481 CA ALA A 80 30.745 -4.018 36.644 1.00 35.36 C +ATOM 486 CA ASP A 81 30.359 -7.373 34.872 1.00 38.72 C +ATOM 494 CA GLY A 82 28.308 -10.332 36.110 1.00 45.79 C +ATOM 498 CA VAL A 83 25.820 -10.242 39.001 1.00 52.24 C +ATOM 505 CA ASP A 84 25.838 -10.250 42.834 1.00 60.54 C +ATOM 513 CA LYS A 85 25.014 -13.158 45.196 1.00 66.72 C +ATOM 522 CA ASN A 86 21.414 -13.062 43.904 1.00 67.37 C +ATOM 530 CA GLY A 87 21.724 -13.423 40.136 1.00 64.74 C +ATOM 534 CA LYS A 88 20.971 -9.733 39.570 1.00 61.12 C +ATOM 543 CA PRO A 89 23.054 -7.201 37.561 1.00 54.68 C +ATOM 550 CA HIS A 90 25.224 -4.957 39.755 1.00 44.44 C +ATOM 560 CA LYS A 91 23.940 -1.433 40.260 1.00 40.48 C +ATOM 569 CA VAL A 92 25.803 1.546 38.843 1.00 38.45 C +ATOM 576 CA ARG A 93 28.709 2.986 40.828 1.00 38.93 C +ATOM 587 CA LEU A 94 29.778 6.584 40.096 1.00 34.37 C +ATOM 595 CA TYR A 95 33.309 7.878 39.513 1.00 30.27 C +ATOM 607 CA SER A 96 34.425 11.475 39.057 1.00 29.44 C +ATOM 613 CA ILE A 97 36.029 12.090 35.662 1.00 27.61 C +ATOM 621 CA ALA A 98 39.769 12.693 36.069 1.00 31.12 C +ATOM 626 CA SER A 99 40.393 13.712 32.475 1.00 32.42 C +ATOM 632 CA SER A 100 39.566 17.142 31.059 1.00 36.14 C +ATOM 638 CA ALA A 101 37.097 17.367 28.154 1.00 41.07 C +ATOM 643 CA ILE A 102 39.764 16.549 25.527 1.00 47.65 C +ATOM 651 CA GLY A 103 41.172 13.692 27.599 1.00 46.77 C +ATOM 655 CA ASP A 104 44.730 12.612 28.289 1.00 43.82 C +ATOM 663 CA PHE A 105 45.115 12.065 24.522 1.00 41.52 C +ATOM 674 CA GLY A 106 43.862 15.455 23.328 1.00 41.66 C +ATOM 678 CA ASP A 107 41.355 13.883 20.926 1.00 40.90 C +ATOM 686 CA SER A 108 38.132 14.250 22.954 1.00 42.95 C +ATOM 692 CA LYS A 109 37.967 10.535 22.224 1.00 44.74 C +ATOM 701 CA THR A 110 38.731 9.184 25.704 1.00 41.09 C +ATOM 708 CA VAL A 111 37.728 9.519 29.374 1.00 39.03 C +ATOM 715 CA SER A 112 39.912 8.705 32.399 1.00 37.17 C +ATOM 721 CA LEU A 113 39.098 7.476 35.935 1.00 32.10 C +ATOM 729 CA CYS A 114 40.964 7.578 39.261 1.00 30.65 C +ATOM 735 CA VAL A 115 39.724 4.459 41.060 1.00 33.45 C +ATOM 742 CA LYS A 116 40.668 3.524 44.628 1.00 34.75 C +ATOM 751 CA ARG A 117 40.376 -0.250 45.123 1.00 32.85 C +ATOM 762 CA LEU A 118 38.137 -1.094 48.077 1.00 30.50 C +ATOM 770 CA ILE A 119 39.376 -3.752 50.459 1.00 34.34 C +ATOM 778 CA TYR A 120 38.699 -4.266 54.125 1.00 31.39 C +ATOM 790 CA THR A 121 38.264 -7.086 56.567 1.00 28.83 C +ATOM 797 CA ASN A 122 34.792 -7.477 58.109 1.00 26.51 C +ATOM 805 CA ASP A 123 33.626 -8.382 61.634 1.00 31.58 C +ATOM 813 CA ALA A 124 34.191 -12.077 60.901 1.00 27.84 C +ATOM 818 CA GLY A 125 37.759 -11.844 59.728 1.00 32.39 C +ATOM 822 CA GLU A 126 36.809 -12.146 56.073 1.00 35.82 C +ATOM 831 CA ILE A 127 38.655 -9.932 53.598 1.00 38.42 C +ATOM 839 CA VAL A 128 36.025 -8.261 51.421 1.00 33.73 C +ATOM 846 CA LYS A 129 36.482 -6.484 48.090 1.00 31.87 C +ATOM 855 CA GLY A 130 34.363 -3.680 46.686 1.00 26.91 C +ATOM 859 CA VAL A 131 32.680 -5.051 43.569 1.00 27.89 C +ATOM 866 CA CYS A 132 33.074 -2.246 41.018 1.00 28.46 C +ATOM 872 CA SER A 133 36.266 -0.553 42.213 1.00 31.33 C +ATOM 878 CA ASN A 134 37.861 -3.983 41.984 1.00 30.29 C +ATOM 886 CA PHE A 135 36.318 -4.795 38.623 1.00 31.48 C +ATOM 897 CA LEU A 136 37.926 -1.553 37.520 1.00 27.81 C +ATOM 905 CA CYS A 137 41.417 -1.976 38.955 1.00 25.91 C +ATOM 911 CA ASP A 138 41.605 -5.419 37.338 1.00 30.22 C +ATOM 919 CA LEU A 139 40.462 -4.306 33.874 1.00 32.69 C +ATOM 927 CA GLN A 140 42.851 -5.511 31.186 1.00 36.80 C +ATOM 936 CA PRO A 141 43.380 -3.220 28.170 1.00 36.16 C +ATOM 943 CA GLY A 142 40.864 -4.420 25.586 1.00 31.10 C +ATOM 947 CA ASP A 143 38.129 -5.298 28.055 1.00 30.62 C +ATOM 955 CA ASN A 144 34.690 -3.847 27.645 1.00 33.52 C +ATOM 963 CA VAL A 145 33.430 -1.522 30.361 1.00 37.08 C +ATOM 970 CA GLN A 146 29.817 -0.374 30.523 1.00 37.65 C +ATOM 979 CA ILE A 147 29.547 3.413 31.045 1.00 30.95 C +ATOM 987 CA THR A 148 26.637 5.791 31.832 1.00 29.95 C +ATOM 994 CA GLY A 149 26.297 9.581 31.843 1.00 32.81 C +ATOM 998 CA PRO A 150 27.785 12.148 31.800 1.00 34.98 C +ATOM 1005 CA VAL A 151 26.376 12.668 35.275 1.00 36.53 C +ATOM 1012 CA GLY A 152 26.196 15.756 37.474 1.00 43.09 C +ATOM 1016 CA LYS A 153 26.048 19.528 37.068 1.00 48.37 C +ATOM 1025 CA GLU A 154 26.921 20.540 40.633 1.00 49.70 C +ATOM 1034 CA MET A 155 30.710 20.266 40.235 1.00 47.30 C +ATOM 1042 CA LEU A 156 30.882 22.020 36.869 1.00 50.36 C +ATOM 1050 CA MET A 157 33.362 24.883 36.404 1.00 55.29 C +ATOM 1058 CA PRO A 158 32.521 28.612 36.605 1.00 54.88 C +ATOM 1065 CA LYS A 159 32.291 30.776 33.464 1.00 54.92 C +ATOM 1074 CA ASP A 160 34.497 33.503 34.939 1.00 57.22 C +ATOM 1082 CA PRO A 161 38.055 32.687 33.759 1.00 58.62 C +ATOM 1089 CA ASN A 162 39.524 35.240 36.163 1.00 60.44 C +ATOM 1097 CA ALA A 163 37.814 33.910 39.279 1.00 55.80 C +ATOM 1102 CA THR A 164 39.596 32.487 42.316 1.00 51.04 C +ATOM 1109 CA ILE A 165 38.966 28.771 42.756 1.00 50.26 C +ATOM 1117 CA ILE A 166 39.774 26.773 45.885 1.00 47.54 C +ATOM 1125 CA MET A 167 39.883 23.014 45.324 1.00 46.38 C +ATOM 1133 CA LEU A 168 39.700 20.963 48.522 1.00 42.18 C +ATOM 1141 CA ALA A 169 40.377 17.316 47.770 1.00 36.41 C +ATOM 1146 CA THR A 170 41.005 14.086 49.622 1.00 32.98 C +ATOM 1153 CA GLY A 171 42.027 10.802 48.014 1.00 31.36 C +ATOM 1157 CA THR A 172 40.386 10.037 44.680 1.00 30.48 C +ATOM 1164 CA GLY A 173 38.640 13.335 45.359 1.00 33.99 C +ATOM 1168 CA ILE A 174 41.418 15.036 43.394 1.00 35.66 C +ATOM 1176 CA ALA A 175 39.758 13.585 40.300 1.00 36.00 C +ATOM 1181 CA PRO A 176 37.445 16.385 39.155 1.00 39.41 C +ATOM 1188 CA PHE A 177 40.109 18.971 39.976 1.00 43.21 C +ATOM 1199 CA ARG A 178 42.726 17.119 37.955 1.00 41.09 C +ATOM 1210 CA SER A 179 40.235 17.536 35.124 1.00 39.92 C +ATOM 1216 CA PHE A 180 39.808 21.204 36.009 1.00 39.23 C +ATOM 1227 CA LEU A 181 43.528 21.949 35.995 1.00 39.50 C +ATOM 1235 CA TRP A 182 44.305 20.081 32.770 1.00 41.47 C +ATOM 1249 CA LYS A 183 42.141 22.654 30.972 1.00 48.08 C +ATOM 1258 CA MET A 184 43.477 25.547 33.062 1.00 52.79 C +ATOM 1266 CA PHE A 185 47.102 25.043 32.014 1.00 57.35 C +ATOM 1277 CA PHE A 186 48.075 21.921 30.051 1.00 55.98 C +ATOM 1288 CA GLU A 187 45.758 23.173 27.297 1.00 54.44 C +ATOM 1297 CA LYS A 188 44.908 26.236 25.196 1.00 51.29 C +ATOM 1306 CA HIS A 189 41.395 27.080 24.003 1.00 51.35 C +ATOM 1316 CA ASP A 190 40.108 29.972 21.873 1.00 54.30 C +ATOM 1324 CA ASP A 191 37.199 30.481 24.249 1.00 53.95 C +ATOM 1332 CA TYR A 192 38.816 29.937 27.634 1.00 50.68 C +ATOM 1344 CA LYS A 193 41.916 31.388 29.230 1.00 51.00 C +ATOM 1353 CA PHE A 194 42.322 30.967 32.956 1.00 52.09 C +ATOM 1364 CA ASN A 195 43.672 34.234 34.312 1.00 56.46 C +ATOM 1372 CA GLY A 196 42.616 34.078 37.969 1.00 57.17 C +ATOM 1376 CA LEU A 197 43.874 31.920 40.843 1.00 57.92 C +ATOM 1384 CA GLY A 198 43.549 28.151 41.086 1.00 56.67 C +ATOM 1388 CA TRP A 199 44.258 26.886 44.592 1.00 51.55 C +ATOM 1402 CA LEU A 200 44.411 23.170 45.379 1.00 49.17 C +ATOM 1410 CA PHE A 201 44.558 21.335 48.709 1.00 48.60 C +ATOM 1421 CA LEU A 202 45.122 17.570 48.598 1.00 45.34 C +ATOM 1429 CA GLY A 203 44.885 15.480 51.742 1.00 48.55 C +ATOM 1433 CA VAL A 204 46.225 11.936 51.755 1.00 50.23 C +ATOM 1440 CA PRO A 205 47.942 9.740 54.365 1.00 51.51 C +ATOM 1447 CA THR A 206 51.284 9.148 52.648 1.00 50.21 C +ATOM 1454 CA SER A 207 53.551 10.483 49.894 1.00 49.38 C +ATOM 1460 CA SER A 208 53.267 7.061 48.259 1.00 43.49 C +ATOM 1466 CA SER A 209 49.588 8.049 48.093 1.00 42.57 C +ATOM 1472 CA LEU A 210 49.990 11.424 46.364 1.00 42.65 C +ATOM 1480 CA LEU A 211 48.121 11.446 43.035 1.00 39.33 C +ATOM 1488 CA TYR A 212 49.516 13.214 39.935 1.00 40.89 C +ATOM 1500 CA LYS A 213 52.128 15.234 41.873 1.00 45.88 C +ATOM 1509 CA GLU A 214 54.518 15.406 38.899 1.00 53.22 C +ATOM 1518 CA GLU A 215 51.680 16.911 36.889 1.00 55.16 C +ATOM 1527 CA PHE A 216 50.757 19.475 39.514 1.00 60.55 C +ATOM 1538 CA GLY A 217 54.488 20.153 39.524 1.00 66.64 C +ATOM 1542 CA LYS A 218 54.575 21.110 35.850 1.00 68.86 C +ATOM 1551 CA MET A 219 51.398 23.159 36.265 1.00 66.97 C +ATOM 1559 CA LYS A 220 53.138 25.090 39.061 1.00 65.97 C +ATOM 1568 CA GLU A 221 55.654 26.250 36.459 1.00 70.02 C +ATOM 1577 CA ARG A 222 53.584 26.507 33.294 1.00 73.48 C +ATOM 1588 CA ALA A 223 52.005 29.449 35.175 1.00 76.21 C +ATOM 1593 CA PRO A 224 53.272 29.877 38.804 1.00 79.25 C +ATOM 1600 CA GLU A 225 51.296 33.124 39.020 1.00 81.84 C +ATOM 1609 CA ASN A 226 47.873 31.528 38.622 1.00 78.84 C +ATOM 1617 CA PHE A 227 48.418 28.176 40.350 1.00 75.28 C +ATOM 1628 CA ARG A 228 49.090 27.305 43.996 1.00 72.05 C +ATOM 1639 CA VAL A 229 49.165 23.724 45.323 1.00 68.82 C +ATOM 1646 CA ASP A 230 49.258 22.581 48.958 1.00 66.54 C +ATOM 1654 CA TYR A 231 49.605 18.943 49.968 1.00 60.31 C +ATOM 1666 CA ALA A 232 48.551 17.560 53.332 1.00 57.39 C +ATOM 1671 CA VAL A 233 50.260 14.228 53.945 1.00 57.14 C +ATOM 1678 CA SER A 234 48.465 13.579 57.244 1.00 60.81 C +ATOM 1684 CA ARG A 235 50.959 11.010 58.514 1.00 60.74 C +ATOM 1695 CA GLU A 236 54.268 12.594 57.481 1.00 59.17 C +ATOM 1704 CA GLN A 237 53.494 16.197 58.450 1.00 59.62 C +ATOM 1713 CA THR A 238 52.590 18.236 61.521 1.00 63.18 C +ATOM 1720 CA ASN A 239 52.019 21.937 62.188 1.00 66.71 C +ATOM 1728 CA ALA A 240 52.096 23.767 65.537 1.00 70.06 C +ATOM 1733 CA ALA A 241 51.302 21.400 68.410 1.00 72.44 C +ATOM 1738 CA GLY A 242 52.383 18.324 66.438 1.00 72.38 C +ATOM 1742 CA GLU A 243 48.826 18.169 65.110 1.00 69.71 C +ATOM 1751 CA ARG A 244 48.674 15.776 62.148 1.00 67.21 C +ATOM 1762 CA MET A 245 48.712 17.796 58.933 1.00 64.20 C +ATOM 1770 CA TYR A 246 45.246 17.082 57.556 1.00 60.65 C +ATOM 1782 CA ILE A 247 43.617 18.437 54.409 1.00 62.98 C +ATOM 1790 CA GLN A 248 42.035 21.001 56.761 1.00 64.64 C +ATOM 1799 CA THR A 249 45.057 21.461 59.009 1.00 63.37 C +ATOM 1806 CA ARG A 250 46.891 22.664 55.903 1.00 62.47 C +ATOM 1817 CA MET A 251 44.123 25.201 55.251 1.00 63.35 C +ATOM 1825 CA ALA A 252 44.571 26.305 58.854 1.00 65.73 C +ATOM 1830 CA GLU A 253 47.973 27.809 58.076 1.00 65.97 C +ATOM 1839 CA TYR A 254 46.267 30.063 55.517 1.00 65.83 C +ATOM 1851 CA LYS A 255 42.991 30.559 57.379 1.00 70.30 C +ATOM 1860 CA GLU A 256 43.578 34.326 57.320 1.00 73.73 C +ATOM 1869 CA GLU A 257 44.189 34.738 53.593 1.00 71.52 C +ATOM 1878 CA LEU A 258 41.459 32.202 52.893 1.00 73.38 C +ATOM 1886 CA TRP A 259 38.790 34.074 54.853 1.00 76.72 C +ATOM 1900 CA GLU A 260 39.721 37.275 53.006 1.00 78.61 C +ATOM 1909 CA LEU A 261 38.580 35.553 49.815 1.00 75.71 C +ATOM 1917 CA LEU A 262 35.391 33.881 51.047 1.00 73.74 C +ATOM 1925 CA LYS A 263 33.562 37.165 50.535 1.00 73.64 C +ATOM 1934 CA LYS A 264 34.299 38.143 46.954 1.00 72.48 C +ATOM 1943 CA ASP A 265 31.954 37.554 43.993 1.00 69.65 C +ATOM 1951 CA ASN A 266 34.660 35.649 42.106 1.00 65.06 C +ATOM 1959 CA THR A 267 35.835 33.117 44.683 1.00 58.24 C +ATOM 1966 CA TYR A 268 34.459 29.646 43.909 1.00 51.04 C +ATOM 1978 CA VAL A 269 35.192 26.827 46.382 1.00 44.95 C +ATOM 1985 CA TYR A 270 35.012 23.150 45.368 1.00 44.96 C +ATOM 1997 CA MET A 271 35.162 20.122 47.656 1.00 41.72 C +ATOM 2005 CA CYS A 272 35.314 16.468 46.632 1.00 37.19 C +ATOM 2011 CA GLY A 273 36.343 13.080 47.951 1.00 37.65 C +ATOM 2015 CA LEU A 274 36.040 10.886 51.020 1.00 39.39 C +ATOM 2023 CA LYS A 275 33.076 12.283 52.955 1.00 44.86 C +ATOM 2032 CA GLY A 276 34.322 13.183 56.400 1.00 49.16 C +ATOM 2036 CA MET A 277 36.932 15.608 55.168 1.00 53.30 C +ATOM 2044 CA GLU A 278 33.917 17.921 55.165 1.00 56.74 C +ATOM 2053 CA LYS A 279 33.531 18.089 58.947 1.00 59.30 C +ATOM 2062 CA GLY A 280 36.982 19.413 59.776 1.00 58.94 C +ATOM 2066 CA ILE A 281 36.705 22.048 57.063 1.00 61.43 C +ATOM 2074 CA ASP A 282 33.453 23.402 58.515 1.00 67.06 C +ATOM 2082 CA ASP A 283 35.050 23.189 61.972 1.00 74.12 C +ATOM 2090 CA ILE A 284 37.991 25.422 61.040 1.00 78.49 C +ATOM 2098 CA MET A 285 35.456 27.566 59.201 1.00 82.25 C +ATOM 2106 CA VAL A 286 32.941 27.959 62.027 1.00 83.44 C +ATOM 2113 CA SER A 287 35.610 29.113 64.469 1.00 83.43 C +ATOM 2119 CA LEU A 288 36.927 31.601 61.887 1.00 85.53 C +ATOM 2127 CA ALA A 289 33.506 33.025 60.970 1.00 86.85 C +ATOM 2132 CA GLU A 290 31.841 32.696 64.387 1.00 89.26 C +ATOM 2141 CA LYS A 291 34.438 35.312 65.347 1.00 88.73 C +ATOM 2150 CA ASP A 292 33.635 37.891 62.652 1.00 88.03 C +ATOM 2158 CA GLY A 293 30.219 37.450 61.081 1.00 87.88 C +ATOM 2162 CA ILE A 294 27.319 35.051 61.511 1.00 84.61 C +ATOM 2170 CA ASP A 295 27.665 31.329 62.188 1.00 82.45 C +ATOM 2178 CA TRP A 296 29.539 29.627 59.355 1.00 80.12 C +ATOM 2192 CA PHE A 297 26.527 27.452 58.512 1.00 78.99 C +ATOM 2203 CA ASP A 298 24.167 30.241 57.486 1.00 76.37 C +ATOM 2211 CA TYR A 299 27.074 31.748 55.561 1.00 74.07 C +ATOM 2223 CA LYS A 300 27.679 28.620 53.473 1.00 74.31 C +ATOM 2232 CA LYS A 301 24.059 29.146 52.464 1.00 75.97 C +ATOM 2241 CA GLN A 302 24.921 32.563 51.018 1.00 75.38 C +ATOM 2250 CA LEU A 303 27.896 31.099 49.155 1.00 72.10 C +ATOM 2258 CA LYS A 304 25.917 28.207 47.690 1.00 72.08 C +ATOM 2267 CA ARG A 305 23.595 31.021 46.594 1.00 74.82 C +ATOM 2278 CA GLY A 306 26.071 32.136 43.958 1.00 71.84 C +ATOM 2282 CA ASP A 307 27.505 28.682 43.220 1.00 67.23 C +ATOM 2290 CA GLN A 308 30.620 29.291 45.346 1.00 60.18 C +ATOM 2299 CA TRP A 309 30.585 26.177 47.537 1.00 52.25 C +ATOM 2313 CA ASN A 310 29.894 22.997 45.597 1.00 45.03 C +ATOM 2321 CA VAL A 311 30.327 19.716 47.403 1.00 39.13 C +ATOM 2328 CA GLU A 312 30.507 16.190 46.110 1.00 35.17 C +ATOM 2337 CA VAL A 313 31.761 13.957 48.861 1.00 30.12 C +ATOM 2344 CA TYR A 314 31.112 10.230 49.021 1.00 28.23 C +ATOM 2358 CA ALA B 1 2.311 24.702 44.475 1.00 74.17 C +ATOM 2363 CA THR B 2 3.590 24.207 48.055 1.00 74.76 C +ATOM 2370 CA TYR B 3 3.069 20.876 49.837 1.00 73.52 C +ATOM 2382 CA ASN B 4 3.748 19.874 53.435 1.00 75.75 C +ATOM 2390 CA VAL B 5 6.618 17.399 53.868 1.00 75.95 C +ATOM 2397 CA LYS B 6 7.769 15.523 56.983 1.00 77.70 C +ATOM 2406 CA LEU B 7 11.351 14.325 57.458 1.00 78.91 C +ATOM 2414 CA ILE B 8 11.807 11.511 59.985 1.00 81.00 C +ATOM 2422 CA THR B 9 15.560 12.046 60.247 1.00 87.49 C +ATOM 2429 CA PRO B 10 17.662 9.793 62.539 1.00 92.94 C +ATOM 2436 CA GLU B 11 18.161 13.147 64.282 1.00 96.61 C +ATOM 2445 CA GLY B 12 14.579 14.154 65.041 1.00 97.52 C +ATOM 2449 CA GLU B 13 11.602 14.823 62.748 1.00 96.90 C +ATOM 2458 CA VAL B 14 11.547 17.892 60.480 1.00 96.63 C +ATOM 2465 CA GLU B 15 8.340 19.701 59.440 1.00 94.86 C +ATOM 2474 CA LEU B 16 9.471 21.479 56.254 1.00 91.55 C +ATOM 2482 CA GLN B 17 7.281 23.141 53.598 1.00 89.75 C +ATOM 2491 CA VAL B 18 8.485 22.069 50.145 1.00 87.92 C +ATOM 2498 CA PRO B 19 6.906 23.558 46.964 1.00 86.35 C +ATOM 2505 CA ASP B 20 5.990 21.744 43.717 1.00 86.29 C +ATOM 2513 CA ASP B 21 8.578 22.751 41.083 1.00 83.78 C +ATOM 2521 CA VAL B 22 11.385 22.401 43.639 1.00 80.98 C +ATOM 2528 CA TYR B 23 13.439 19.280 44.481 1.00 77.04 C +ATOM 2540 CA ILE B 24 13.212 18.196 48.120 1.00 76.45 C +ATOM 2548 CA LEU B 25 16.959 18.133 48.851 1.00 75.15 C +ATOM 2556 CA ASP B 26 17.154 21.745 47.689 1.00 75.80 C +ATOM 2564 CA GLN B 27 14.616 22.906 50.280 1.00 76.31 C +ATOM 2573 CA ALA B 28 16.562 20.957 52.914 1.00 78.86 C +ATOM 2578 CA GLU B 29 19.698 23.011 52.198 1.00 81.51 C +ATOM 2587 CA GLU B 30 17.491 26.106 52.510 1.00 83.25 C +ATOM 2596 CA ASP B 31 15.857 25.933 55.935 1.00 81.92 C +ATOM 2604 CA GLY B 32 19.280 24.859 57.151 1.00 79.08 C +ATOM 2608 CA ILE B 33 18.621 21.130 57.157 1.00 76.93 C +ATOM 2616 CA ASP B 34 21.528 18.731 56.618 1.00 73.53 C +ATOM 2624 CA LEU B 35 20.738 15.738 54.421 1.00 67.74 C +ATOM 2632 CA PRO B 36 23.138 13.391 52.547 1.00 65.90 C +ATOM 2639 CA TYR B 37 23.916 14.226 48.912 1.00 64.85 C +ATOM 2651 CA SER B 38 26.659 13.373 46.412 1.00 62.58 C +ATOM 2657 CA CYS B 39 26.193 13.603 42.652 1.00 60.99 C +ATOM 2663 CA ARG B 40 22.908 15.441 43.251 1.00 58.35 C +ATOM 2674 CA ALA B 41 21.699 14.108 39.886 1.00 56.38 C +ATOM 2679 CA GLY B 42 19.886 10.955 40.991 1.00 56.66 C +ATOM 2683 CA SER B 43 22.465 8.336 40.010 1.00 58.55 C +ATOM 2689 CA CYS B 44 23.548 7.052 43.447 1.00 56.27 C +ATOM 2695 CA SER B 45 22.057 5.987 46.791 1.00 58.20 C +ATOM 2701 CA SER B 46 23.574 8.773 48.890 1.00 59.13 C +ATOM 2707 CA CYS B 47 20.220 10.475 49.517 1.00 65.64 C +ATOM 2713 CA ALA B 48 17.911 7.436 49.610 1.00 69.71 C +ATOM 2718 CA GLY B 49 14.733 7.635 51.681 1.00 73.09 C +ATOM 2722 CA LYS B 50 11.712 5.340 52.183 1.00 73.77 C +ATOM 2731 CA VAL B 51 8.551 7.412 51.568 1.00 76.51 C +ATOM 2738 CA VAL B 52 5.237 7.081 53.429 1.00 78.85 C +ATOM 2745 CA SER B 53 2.180 9.376 53.647 1.00 79.57 C +ATOM 2751 CA GLY B 54 2.118 10.991 50.218 1.00 76.32 C +ATOM 2755 CA SER B 55 3.577 10.944 46.726 1.00 76.31 C +ATOM 2761 CA VAL B 56 6.436 12.592 44.828 1.00 77.50 C +ATOM 2768 CA ASP B 57 7.691 12.960 41.243 1.00 76.83 C +ATOM 2776 CA GLN B 58 11.150 11.483 40.555 1.00 76.66 C +ATOM 2785 CA SER B 59 10.976 10.827 36.792 1.00 80.19 C +ATOM 2791 CA ASP B 60 14.688 11.644 36.510 1.00 83.51 C +ATOM 2799 CA GLN B 61 15.175 8.137 37.916 1.00 85.74 C +ATOM 2808 CA SER B 62 18.644 7.080 36.699 1.00 85.85 C +ATOM 2814 CA TYR B 63 19.324 5.049 39.852 1.00 84.49 C +ATOM 2826 CA LEU B 64 15.683 4.296 40.629 1.00 89.06 C +ATOM 2834 CA ASP B 65 15.356 0.604 39.742 1.00 92.21 C +ATOM 2842 CA ASP B 66 12.421 -1.791 39.331 1.00 92.35 C +ATOM 2850 CA GLY B 67 10.747 -2.542 42.659 1.00 89.07 C +ATOM 2854 CA GLN B 68 12.336 0.632 44.010 1.00 88.41 C +ATOM 2863 CA ILE B 69 9.483 2.828 42.742 1.00 86.11 C +ATOM 2871 CA ALA B 70 7.060 0.441 44.446 1.00 81.10 C +ATOM 2876 CA ASP B 71 8.985 -0.310 47.648 1.00 76.82 C +ATOM 2884 CA GLY B 72 8.653 3.423 48.186 1.00 73.00 C +ATOM 2888 CA TRP B 73 12.342 4.386 48.095 1.00 67.93 C +ATOM 2902 CA VAL B 74 13.052 8.007 47.136 1.00 63.84 C +ATOM 2909 CA LEU B 75 16.093 9.940 45.892 1.00 58.37 C +ATOM 2917 CA THR B 76 15.524 13.198 47.826 1.00 55.82 C +ATOM 2924 CA CYS B 77 17.941 15.109 45.556 1.00 58.23 C +ATOM 2930 CA HIS B 78 15.777 14.389 42.513 1.00 64.55 C +ATOM 2940 CA ALA B 79 12.108 14.429 43.512 1.00 68.40 C +ATOM 2945 CA TYR B 80 9.442 17.152 43.581 1.00 69.69 C +ATOM 2957 CA PRO B 81 6.414 16.584 45.842 1.00 71.39 C +ATOM 2964 CA THR B 82 3.015 16.014 44.179 1.00 73.67 C +ATOM 2971 CA SER B 83 1.278 15.771 47.557 1.00 76.90 C +ATOM 2977 CA ASP B 84 1.940 16.119 51.289 1.00 75.20 C +ATOM 2985 CA VAL B 85 4.840 13.765 52.050 1.00 71.37 C +ATOM 2992 CA VAL B 86 6.363 11.824 54.956 1.00 70.12 C +ATOM 2999 CA ILE B 87 9.770 10.300 54.188 1.00 74.18 C +ATOM 3007 CA GLU B 88 12.211 8.403 56.410 1.00 78.53 C +ATOM 3012 CA THR B 89 15.541 9.964 55.407 1.00 79.79 C +ATOM 3019 CA HIS B 90 19.062 8.538 55.881 1.00 79.40 C +ATOM 3029 CA LYS B 91 17.584 5.099 55.099 1.00 84.52 C +ATOM 3038 CA GLU B 92 20.016 2.596 53.549 1.00 91.64 C +ATOM 3047 CA GLU B 93 20.192 -0.858 51.981 1.00 98.97 C +ATOM 3056 CA GLU B 94 23.321 -2.924 51.298 1.00106.32 C +ATOM 3065 CA LEU B 95 22.104 -6.552 51.453 1.00111.32 C +ATOM 3073 CA THR B 96 18.778 -8.417 51.866 1.00116.01 C +ATOM 3080 CA GLY B 97 18.877 -11.302 49.394 1.00116.63 C +ATOM 3084 CA ALA B 98 22.056 -9.833 47.910 1.00116.02 C +ATOM 3091 CA GLU C 19 26.080 -2.480 15.294 1.00 73.96 C +ATOM 3100 CA SER C 20 23.405 0.198 14.956 1.00 67.27 C +ATOM 3106 CA LYS C 21 22.937 3.927 15.380 1.00 59.27 C +ATOM 3115 CA LYS C 22 19.198 3.481 15.874 1.00 58.42 C +ATOM 3124 CA GLN C 23 17.251 3.141 19.137 1.00 59.89 C +ATOM 3133 CA GLU C 24 17.931 -0.276 20.610 1.00 62.66 C +ATOM 3142 CA GLU C 25 16.850 -0.453 24.226 1.00 64.27 C +ATOM 3151 CA GLY C 26 13.211 -0.817 25.116 1.00 61.78 C +ATOM 3155 CA VAL C 27 12.703 -2.073 21.582 1.00 58.37 C +ATOM 3162 CA VAL C 28 10.779 -5.347 21.485 1.00 54.17 C +ATOM 3169 CA THR C 29 9.481 -7.339 18.549 1.00 52.79 C +ATOM 3176 CA ASN C 30 6.670 -9.775 17.786 1.00 51.30 C +ATOM 3184 CA LEU C 31 4.863 -9.997 21.112 1.00 51.05 C +ATOM 3192 CA TYR C 32 1.766 -11.297 19.327 1.00 50.51 C +ATOM 3204 CA LYS C 33 1.373 -13.532 16.266 1.00 49.49 C +ATOM 3213 CA PRO C 34 -1.609 -14.150 13.925 1.00 50.98 C +ATOM 3220 CA LYS C 35 -2.450 -17.248 16.011 1.00 55.46 C +ATOM 3229 CA GLU C 36 -2.977 -15.400 19.288 1.00 53.79 C +ATOM 3238 CA PRO C 37 -3.251 -11.638 18.607 1.00 49.32 C +ATOM 3245 CA TYR C 38 -3.674 -9.050 21.318 1.00 46.76 C +ATOM 3257 CA VAL C 39 -7.276 -7.947 21.418 1.00 43.68 C +ATOM 3264 CA GLY C 40 -7.415 -4.194 21.922 1.00 41.62 C +ATOM 3268 CA ARG C 41 -10.273 -1.719 21.954 1.00 40.07 C +ATOM 3279 CA CYS C 42 -11.026 1.064 19.477 1.00 36.37 C +ATOM 3285 CA LEU C 43 -11.330 4.206 21.583 1.00 31.09 C +ATOM 3293 CA LEU C 44 -11.337 6.671 18.673 1.00 28.46 C +ATOM 3301 CA ASN C 45 -11.792 6.653 14.923 1.00 26.74 C +ATOM 3309 CA THR C 46 -11.954 9.920 13.013 1.00 25.29 C +ATOM 3316 CA LYS C 47 -11.667 10.775 9.352 1.00 21.50 C +ATOM 3325 CA ILE C 48 -8.895 13.355 9.121 1.00 19.33 C +ATOM 3333 CA THR C 49 -9.125 14.281 5.442 1.00 20.38 C +ATOM 3340 CA GLY C 50 -11.630 16.676 3.855 1.00 20.12 C +ATOM 3344 CA ASP C 51 -14.895 15.345 2.412 1.00 21.75 C +ATOM 3352 CA ASP C 52 -13.889 16.693 -0.999 1.00 21.19 C +ATOM 3360 CA ALA C 53 -10.651 14.683 -0.749 1.00 21.06 C +ATOM 3365 CA PRO C 54 -10.036 11.974 -3.413 1.00 21.39 C +ATOM 3372 CA GLY C 55 -9.982 9.067 -0.977 1.00 24.42 C +ATOM 3376 CA GLU C 56 -10.374 9.298 2.857 1.00 22.08 C +ATOM 3385 CA THR C 57 -7.723 8.611 5.517 1.00 20.31 C +ATOM 3392 CA TRP C 58 -8.541 7.849 9.162 1.00 19.33 C +ATOM 3406 CA HIS C 59 -6.758 8.520 12.438 1.00 22.68 C +ATOM 3416 CA MET C 60 -7.645 5.951 15.108 1.00 27.16 C +ATOM 3424 CA VAL C 61 -6.672 5.224 18.723 1.00 29.32 C +ATOM 3431 CA PHE C 62 -6.669 1.704 20.220 1.00 34.23 C +ATOM 3442 CA SER C 63 -6.102 0.643 23.847 1.00 37.05 C +ATOM 3448 CA THR C 64 -3.096 -1.517 24.798 1.00 41.86 C +ATOM 3455 CA GLU C 65 -3.169 -1.652 28.621 1.00 48.33 C +ATOM 3464 CA GLY C 66 0.537 -0.885 28.318 1.00 52.45 C +ATOM 3468 CA LYS C 67 0.955 -4.385 26.891 1.00 54.14 C +ATOM 3477 CA ILE C 68 2.429 -3.211 23.570 1.00 51.52 C +ATOM 3485 CA PRO C 69 5.602 -1.279 24.487 1.00 49.85 C +ATOM 3492 CA TYR C 70 6.523 -0.180 20.967 1.00 44.48 C +ATOM 3504 CA ARG C 71 9.185 2.353 19.993 1.00 40.96 C +ATOM 3515 CA GLU C 72 8.727 5.317 17.688 1.00 33.49 C +ATOM 3524 CA GLY C 73 8.913 3.876 14.164 1.00 30.16 C +ATOM 3528 CA GLN C 74 7.423 0.399 14.427 1.00 31.26 C +ATOM 3537 CA SER C 75 4.187 -0.913 12.966 1.00 33.65 C +ATOM 3543 CA ILE C 76 1.454 -3.212 14.278 1.00 33.75 C +ATOM 3551 CA GLY C 77 -0.295 -5.923 12.356 1.00 34.32 C +ATOM 3555 CA VAL C 78 -4.060 -6.111 12.164 1.00 36.67 C +ATOM 3562 CA ILE C 79 -6.137 -9.230 11.507 1.00 41.91 C +ATOM 3570 CA ALA C 80 -9.427 -8.086 10.024 1.00 44.06 C +ATOM 3575 CA ASP C 81 -12.530 -9.927 11.224 1.00 47.03 C +ATOM 3583 CA GLY C 82 -13.972 -12.487 8.829 1.00 53.52 C +ATOM 3587 CA VAL C 83 -12.521 -14.951 6.324 1.00 62.57 C +ATOM 3594 CA ASP C 84 -11.856 -14.200 2.630 1.00 71.97 C +ATOM 3602 CA LYS C 85 -12.935 -17.403 0.861 1.00 76.86 C +ATOM 3611 CA ASN C 86 -13.690 -18.960 4.253 1.00 76.52 C +ATOM 3619 CA GLY C 87 -10.006 -19.837 4.066 1.00 76.22 C +ATOM 3623 CA LYS C 88 -8.802 -19.138 7.616 1.00 71.60 C +ATOM 3632 CA PRO C 89 -8.651 -15.577 8.944 1.00 64.14 C +ATOM 3639 CA HIS C 90 -7.547 -12.649 6.805 1.00 52.35 C +ATOM 3649 CA LYS C 91 -3.753 -12.529 6.474 1.00 46.81 C +ATOM 3658 CA VAL C 92 -2.180 -9.868 8.686 1.00 43.48 C +ATOM 3665 CA ARG C 93 -1.491 -6.414 7.232 1.00 36.99 C +ATOM 3676 CA LEU C 94 0.983 -3.882 8.601 1.00 32.95 C +ATOM 3684 CA TYR C 95 0.340 -0.239 9.510 1.00 24.84 C +ATOM 3696 CA SER C 96 3.003 2.101 10.803 1.00 23.32 C +ATOM 3702 CA ILE C 97 2.244 3.502 14.236 1.00 24.12 C +ATOM 3710 CA ALA C 98 1.243 7.179 13.932 1.00 22.32 C +ATOM 3715 CA SER C 99 1.572 7.636 17.676 1.00 25.69 C +ATOM 3721 CA SER C 100 4.752 7.924 19.726 1.00 28.83 C +ATOM 3727 CA ALA C 101 5.741 5.521 22.508 1.00 35.61 C +ATOM 3732 CA ILE C 102 3.906 7.635 25.079 1.00 38.39 C +ATOM 3740 CA GLY C 103 0.899 7.826 22.742 1.00 31.93 C +ATOM 3744 CA ASP C 104 -1.803 10.384 21.986 1.00 28.77 C +ATOM 3752 CA PHE C 105 -3.050 10.293 25.607 1.00 37.05 C +ATOM 3763 CA GLY C 106 0.503 10.389 26.967 1.00 39.36 C +ATOM 3767 CA ASP C 107 -0.221 7.437 29.266 1.00 41.44 C +ATOM 3775 CA SER C 108 1.566 4.766 27.217 1.00 42.18 C +ATOM 3781 CA LYS C 109 -1.747 2.877 27.156 1.00 42.45 C +ATOM 3790 CA THR C 110 -2.698 3.586 23.515 1.00 38.10 C +ATOM 3797 CA VAL C 111 -1.603 2.971 19.906 1.00 32.79 C +ATOM 3804 CA SER C 112 -2.671 5.020 16.872 1.00 29.60 C +ATOM 3810 CA LEU C 113 -2.713 4.324 13.126 1.00 25.68 C +ATOM 3818 CA CYS C 114 -3.142 6.498 9.999 1.00 24.23 C +ATOM 3824 CA VAL C 115 -5.345 4.496 7.641 1.00 22.80 C +ATOM 3831 CA LYS C 116 -6.221 5.196 4.015 1.00 22.11 C +ATOM 3840 CA ARG C 117 -9.458 3.521 2.955 1.00 25.68 C +ATOM 3851 CA LEU C 118 -8.447 1.440 -0.100 1.00 28.80 C +ATOM 3859 CA ILE C 119 -11.140 1.661 -2.792 1.00 31.75 C +ATOM 3867 CA TYR C 120 -10.086 0.716 -6.312 1.00 32.93 C +ATOM 3879 CA THR C 121 -11.388 -0.733 -9.598 1.00 36.84 C +ATOM 3886 CA ASN C 122 -10.258 -4.257 -10.546 1.00 36.90 C +ATOM 3894 CA ASP C 123 -9.574 -5.562 -14.056 1.00 45.45 C +ATOM 3902 CA ALA C 124 -13.196 -6.758 -14.269 1.00 44.66 C +ATOM 3907 CA GLY C 125 -14.207 -3.102 -14.023 1.00 45.49 C +ATOM 3911 CA GLU C 126 -16.059 -3.511 -10.722 1.00 45.54 C +ATOM 3920 CA ILE C 127 -15.507 -1.321 -7.638 1.00 39.70 C +ATOM 3928 CA VAL C 128 -13.846 -3.171 -4.762 1.00 38.09 C +ATOM 3935 CA LYS C 129 -12.759 -2.512 -1.198 1.00 33.77 C +ATOM 3944 CA GLY C 130 -9.566 -3.363 0.599 1.00 31.98 C +ATOM 3948 CA VAL C 131 -10.443 -5.797 3.385 1.00 33.16 C +ATOM 3955 CA CYS C 132 -8.241 -4.645 6.257 1.00 29.97 C +ATOM 3961 CA SER C 133 -8.238 -0.898 5.607 1.00 30.67 C +ATOM 3967 CA ASN C 134 -12.022 -0.902 5.268 1.00 30.35 C +ATOM 3975 CA PHE C 135 -12.375 -2.946 8.424 1.00 29.86 C +ATOM 3986 CA LEU C 136 -10.223 -0.334 10.195 1.00 29.42 C +ATOM 3994 CA CYS C 137 -11.779 2.834 8.813 1.00 32.27 C +ATOM 4000 CA ASP C 138 -15.116 1.280 9.724 1.00 34.29 C +ATOM 4008 CA LEU C 139 -14.287 0.699 13.399 1.00 37.51 C +ATOM 4016 CA GLN C 140 -16.635 2.170 16.028 1.00 43.76 C +ATOM 4025 CA PRO C 141 -15.630 3.032 19.581 1.00 42.77 C +ATOM 4032 CA GLY C 142 -16.082 -0.210 21.478 1.00 42.83 C +ATOM 4036 CA ASP C 143 -15.117 -2.625 18.696 1.00 40.91 C +ATOM 4044 CA ASN C 144 -12.182 -4.947 19.288 1.00 45.66 C +ATOM 4052 CA VAL C 145 -9.056 -5.146 17.145 1.00 46.95 C +ATOM 4059 CA GLN C 146 -6.707 -8.107 16.606 1.00 48.69 C +ATOM 4068 CA ILE C 147 -3.249 -6.538 17.123 1.00 46.84 C +ATOM 4076 CA THR C 148 -0.010 -8.392 16.264 1.00 46.26 C +ATOM 4083 CA GLY C 149 3.543 -7.117 16.634 1.00 45.60 C +ATOM 4087 CA PRO C 150 5.248 -4.818 17.394 1.00 44.97 C +ATOM 4094 CA VAL C 151 7.423 -5.293 14.321 1.00 44.50 C +ATOM 4101 CA GLY C 152 10.289 -3.716 12.438 1.00 45.33 C +ATOM 4105 CA LYS C 153 13.599 -2.161 13.435 1.00 48.64 C +ATOM 4114 CA GLU C 154 14.166 -0.437 10.074 1.00 48.20 C +ATOM 4123 CA MET C 155 12.437 2.888 10.737 1.00 41.77 C +ATOM 4131 CA LEU C 156 13.839 3.081 14.267 1.00 38.27 C +ATOM 4139 CA MET C 157 15.076 6.540 15.308 1.00 34.29 C +ATOM 4147 CA PRO C 158 18.782 7.419 15.339 1.00 34.05 C +ATOM 4154 CA LYS C 159 20.262 7.521 18.845 1.00 35.82 C +ATOM 4163 CA ASP C 160 22.076 10.792 18.273 1.00 35.95 C +ATOM 4171 CA PRO C 161 19.683 13.401 19.809 1.00 35.63 C +ATOM 4178 CA ASN C 162 21.563 15.948 17.758 1.00 33.92 C +ATOM 4186 CA ALA C 163 21.028 14.172 14.487 1.00 30.82 C +ATOM 4191 CA THR C 164 19.693 15.722 11.305 1.00 25.18 C +ATOM 4198 CA ILE C 165 16.617 13.601 10.636 1.00 19.91 C +ATOM 4206 CA ILE C 166 15.351 13.978 7.060 1.00 13.76 C +ATOM 4214 CA MET C 167 11.843 12.550 6.703 1.00 14.98 C +ATOM 4222 CA LEU C 168 10.385 11.831 3.251 1.00 16.64 C +ATOM 4230 CA ALA C 169 6.747 10.808 3.007 1.00 15.85 C +ATOM 4235 CA THR C 170 3.765 10.346 0.737 1.00 14.23 C +ATOM 4242 CA GLY C 171 0.255 9.724 2.035 1.00 13.78 C +ATOM 4246 CA THR C 172 -0.103 7.560 5.139 1.00 17.62 C +ATOM 4253 CA GLY C 173 3.646 7.343 4.821 1.00 17.20 C +ATOM 4257 CA ILE C 174 3.469 10.213 7.270 1.00 15.91 C +ATOM 4265 CA ALA C 175 2.586 7.783 10.110 1.00 15.63 C +ATOM 4270 CA PRO C 176 6.023 6.933 11.582 1.00 17.04 C +ATOM 4277 CA PHE C 177 7.215 10.514 11.327 1.00 18.21 C +ATOM 4288 CA ARG C 178 4.268 11.745 13.359 1.00 22.35 C +ATOM 4299 CA SER C 179 5.563 9.289 15.983 1.00 25.22 C +ATOM 4305 CA PHE C 180 9.139 10.593 15.614 1.00 25.98 C +ATOM 4316 CA LEU C 181 7.925 14.180 15.767 1.00 29.12 C +ATOM 4324 CA TRP C 182 5.625 13.641 18.714 1.00 31.35 C +ATOM 4338 CA LYS C 183 8.488 12.385 20.871 1.00 30.92 C +ATOM 4347 CA MET C 184 10.841 15.050 19.503 1.00 24.85 C +ATOM 4355 CA PHE C 185 8.741 18.202 20.114 1.00 22.97 C +ATOM 4366 CA PHE C 186 5.604 17.337 22.076 1.00 27.77 C +ATOM 4377 CA GLU C 187 7.117 15.432 25.009 1.00 37.71 C +ATOM 4386 CA LYS C 188 9.542 15.977 27.878 1.00 53.59 C +ATOM 4395 CA HIS C 189 12.355 13.416 28.180 1.00 63.67 C +ATOM 4405 CA ASP C 190 15.318 13.181 30.569 1.00 66.93 C +ATOM 4413 CA ASP C 191 17.480 11.106 28.238 1.00 59.79 C +ATOM 4421 CA TYR C 192 16.190 12.725 25.047 1.00 51.96 C +ATOM 4433 CA LYS C 193 16.700 16.406 24.324 1.00 47.01 C +ATOM 4442 CA PHE C 194 16.580 16.471 20.530 1.00 39.85 C +ATOM 4453 CA ASN C 195 18.572 19.494 19.409 1.00 37.52 C +ATOM 4461 CA GLY C 196 19.361 18.548 15.845 1.00 32.08 C +ATOM 4465 CA LEU C 197 17.310 19.266 12.766 1.00 28.26 C +ATOM 4473 CA GLY C 198 14.051 17.526 11.928 1.00 25.05 C +ATOM 4477 CA TRP C 199 13.211 18.137 8.269 1.00 19.81 C +ATOM 4491 CA LEU C 200 9.908 16.742 7.059 1.00 13.86 C +ATOM 4499 CA PHE C 201 8.855 16.521 3.429 1.00 14.83 C +ATOM 4510 CA LEU C 202 5.288 15.361 2.717 1.00 16.12 C +ATOM 4518 CA GLY C 203 3.701 14.731 -0.681 1.00 13.79 C +ATOM 4522 CA VAL C 204 -0.051 14.414 -1.182 1.00 11.75 C +ATOM 4529 CA PRO C 205 -2.113 15.264 -4.308 1.00 14.66 C +ATOM 4536 CA THR C 206 -4.553 17.737 -2.778 1.00 16.37 C +ATOM 4543 CA SER C 207 -4.756 20.169 0.120 1.00 18.01 C +ATOM 4549 CA SER C 208 -7.780 18.225 1.280 1.00 17.59 C +ATOM 4555 CA SER C 209 -5.452 15.198 1.550 1.00 16.19 C +ATOM 4561 CA LEU C 210 -2.972 16.940 3.860 1.00 14.22 C +ATOM 4569 CA LEU C 211 -2.255 14.980 7.059 1.00 14.43 C +ATOM 4577 CA TYR C 212 -1.624 16.449 10.549 1.00 18.94 C +ATOM 4589 CA LYS C 213 -0.818 19.896 9.150 1.00 22.61 C +ATOM 4598 CA GLU C 214 -2.039 21.572 12.352 1.00 25.73 C +ATOM 4607 CA GLU C 215 0.152 19.413 14.514 1.00 19.23 C +ATOM 4616 CA PHE C 216 3.216 20.178 12.439 1.00 17.80 C +ATOM 4627 CA GLY C 217 2.478 23.890 12.512 1.00 19.90 C +ATOM 4631 CA LYS C 218 2.578 24.001 16.294 1.00 25.54 C +ATOM 4640 CA MET C 219 5.810 22.021 16.188 1.00 26.79 C +ATOM 4648 CA LYS C 220 7.224 24.606 13.819 1.00 31.85 C +ATOM 4657 CA GLU C 221 6.071 27.341 16.219 1.00 38.62 C +ATOM 4666 CA ARG C 222 7.760 25.760 19.233 1.00 39.10 C +ATOM 4677 CA ALA C 223 11.124 24.971 17.668 1.00 35.43 C +ATOM 4682 CA PRO C 224 11.696 27.100 14.528 1.00 32.99 C +ATOM 4689 CA GLU C 225 15.425 26.331 14.360 1.00 33.87 C +ATOM 4698 CA ASN C 226 15.038 22.591 14.986 1.00 30.46 C +ATOM 4706 CA PHE C 227 12.088 21.755 12.732 1.00 24.98 C +ATOM 4717 CA ARG C 228 11.351 22.384 9.075 1.00 19.87 C +ATOM 4728 CA VAL C 229 8.435 21.010 7.118 1.00 14.21 C +ATOM 4735 CA ASP C 230 7.739 21.452 3.398 1.00 12.26 C +ATOM 4743 CA TYR C 231 4.627 20.147 1.722 1.00 14.42 C +ATOM 4755 CA ALA C 232 4.334 19.003 -1.872 1.00 9.99 C +ATOM 4760 CA VAL C 233 0.778 19.232 -3.168 1.00 10.49 C +ATOM 4767 CA SER C 234 1.043 17.769 -6.694 1.00 19.00 C +ATOM 4773 CA ARG C 235 -2.240 19.042 -8.206 1.00 23.13 C +ATOM 4784 CA GLU C 236 -2.069 22.459 -6.578 1.00 17.58 C +ATOM 4793 CA GLN C 237 1.546 23.511 -6.623 1.00 15.89 C +ATOM 4802 CA THR C 238 4.202 24.018 -9.275 1.00 17.86 C +ATOM 4809 CA ASN C 239 7.922 24.800 -9.182 1.00 15.15 C +ATOM 4817 CA ALA C 240 9.558 27.791 -10.892 1.00 21.51 C +ATOM 4822 CA ALA C 241 9.475 25.887 -14.174 1.00 24.05 C +ATOM 4827 CA GLY C 242 5.741 25.110 -13.938 1.00 26.25 C +ATOM 4831 CA GLU C 243 5.999 21.359 -13.153 1.00 25.92 C +ATOM 4840 CA ARG C 244 3.679 19.536 -10.704 1.00 24.04 C +ATOM 4851 CA MET C 245 5.076 19.643 -7.174 1.00 18.58 C +ATOM 4859 CA TYR C 246 5.784 16.047 -6.100 1.00 14.16 C +ATOM 4871 CA ILE C 247 7.910 15.343 -3.034 1.00 16.78 C +ATOM 4879 CA GLN C 248 11.089 15.070 -5.120 1.00 18.72 C +ATOM 4888 CA THR C 249 10.168 18.255 -6.921 1.00 20.93 C +ATOM 4895 CA ARG C 250 9.962 20.031 -3.567 1.00 19.25 C +ATOM 4906 CA MET C 251 13.275 18.471 -2.561 1.00 19.40 C +ATOM 4914 CA ALA C 252 14.910 19.812 -5.760 1.00 20.48 C +ATOM 4919 CA GLU C 253 14.456 23.418 -4.569 1.00 18.19 C +ATOM 4928 CA TYR C 254 16.804 22.515 -1.673 1.00 17.80 C +ATOM 4940 CA LYS C 255 19.038 20.415 -3.902 1.00 20.66 C +ATOM 4949 CA GLU C 256 22.452 21.603 -2.682 1.00 16.05 C +ATOM 4958 CA GLU C 257 21.544 21.914 0.993 1.00 15.89 C +ATOM 4967 CA LEU C 258 20.377 18.297 0.919 1.00 20.74 C +ATOM 4975 CA TRP C 259 23.388 16.939 -0.965 1.00 23.45 C +ATOM 4989 CA GLU C 260 25.645 18.669 1.563 1.00 24.08 C +ATOM 4998 CA LEU C 261 23.573 17.378 4.477 1.00 24.74 C +ATOM 5006 CA LEU C 262 24.020 13.928 2.938 1.00 26.14 C +ATOM 5014 CA LYS C 263 27.792 14.091 3.402 1.00 25.40 C +ATOM 5023 CA LYS C 264 27.457 14.521 7.176 1.00 31.47 C +ATOM 5032 CA ASP C 265 27.877 11.474 9.425 1.00 35.31 C +ATOM 5040 CA ASN C 266 24.934 12.482 11.620 1.00 29.63 C +ATOM 5048 CA THR C 267 22.321 12.795 8.832 1.00 28.00 C +ATOM 5055 CA TYR C 268 19.556 10.160 8.808 1.00 27.00 C +ATOM 5067 CA VAL C 269 17.143 9.903 5.884 1.00 24.65 C +ATOM 5074 CA TYR C 270 13.890 8.016 6.276 1.00 23.37 C +ATOM 5086 CA MET C 271 11.373 7.327 3.518 1.00 18.93 C +ATOM 5094 CA CYS C 272 7.834 6.074 4.043 1.00 18.24 C +ATOM 5100 CA GLY C 273 4.784 5.874 1.826 1.00 22.39 C +ATOM 5104 CA LEU C 274 3.837 4.483 -1.568 1.00 26.95 C +ATOM 5112 CA LYS C 275 6.305 2.384 -3.532 1.00 32.36 C +ATOM 5121 CA GLY C 276 7.741 4.199 -6.514 1.00 37.46 C +ATOM 5125 CA MET C 277 7.714 7.455 -4.608 1.00 28.76 C +ATOM 5133 CA GLU C 278 11.430 6.639 -4.425 1.00 32.22 C +ATOM 5142 CA LYS C 279 12.017 6.321 -8.153 1.00 29.94 C +ATOM 5151 CA GLY C 280 11.317 10.057 -8.293 1.00 24.18 C +ATOM 5155 CA ILE C 281 13.766 10.673 -5.460 1.00 23.68 C +ATOM 5163 CA ASP C 282 16.431 8.365 -6.934 1.00 26.58 C +ATOM 5171 CA ASP C 283 16.211 10.530 -10.054 1.00 28.70 C +ATOM 5179 CA ILE C 284 17.089 13.937 -8.538 1.00 27.28 C +ATOM 5187 CA MET C 285 19.706 12.222 -6.388 1.00 27.45 C +ATOM 5195 CA VAL C 286 21.377 10.712 -9.470 1.00 30.74 C +ATOM 5202 CA SER C 287 21.619 14.159 -11.061 1.00 32.14 C +ATOM 5208 CA LEU C 288 23.240 15.463 -7.873 1.00 34.20 C +ATOM 5216 CA ALA C 289 25.801 12.653 -7.874 1.00 40.16 C +ATOM 5221 CA GLU C 290 26.837 12.825 -11.536 1.00 41.84 C +ATOM 5230 CA LYS C 291 27.855 16.387 -10.793 1.00 43.17 C +ATOM 5239 CA ASP C 292 30.299 15.115 -8.139 1.00 41.84 C +ATOM 5247 CA GLY C 293 31.237 12.232 -10.420 1.00 46.12 C +ATOM 5251 CA ILE C 294 30.053 9.669 -7.864 1.00 45.54 C +ATOM 5259 CA ASP C 295 27.399 6.998 -8.480 1.00 41.14 C +ATOM 5267 CA TRP C 296 24.222 7.605 -6.479 1.00 30.67 C +ATOM 5281 CA PHE C 297 23.381 3.910 -6.151 1.00 31.97 C +ATOM 5292 CA ASP C 298 26.856 2.916 -4.907 1.00 38.12 C +ATOM 5300 CA TYR C 299 26.671 5.875 -2.540 1.00 39.05 C +ATOM 5312 CA LYS C 300 23.196 4.971 -1.294 1.00 41.63 C +ATOM 5321 CA LYS C 301 24.542 1.489 -0.577 1.00 43.40 C +ATOM 5330 CA GLN C 302 27.207 3.064 1.608 1.00 43.79 C +ATOM 5339 CA LEU C 303 24.476 5.181 3.238 1.00 41.51 C +ATOM 5347 CA LYS C 304 22.138 2.343 4.264 1.00 45.18 C +ATOM 5356 CA ARG C 305 25.322 0.535 5.256 1.00 46.65 C +ATOM 5367 CA GLY C 306 25.613 3.181 7.945 1.00 40.29 C +ATOM 5371 CA ASP C 307 21.954 3.487 8.940 1.00 41.21 C +ATOM 5379 CA GLN C 308 21.463 6.730 7.023 1.00 35.55 C +ATOM 5388 CA TRP C 309 18.961 5.674 4.361 1.00 31.22 C +ATOM 5402 CA ASN C 310 16.018 3.728 5.752 1.00 31.61 C +ATOM 5410 CA VAL C 311 13.120 2.841 3.452 1.00 32.13 C +ATOM 5417 CA GLU C 312 9.705 1.332 4.261 1.00 31.51 C +ATOM 5426 CA VAL C 313 7.466 1.606 1.209 1.00 26.39 C +ATOM 5433 CA TYR C 314 4.403 -0.343 0.111 1.00 25.42 C diff --git a/examples/appletParameters.html b/examples/appletParameters.html new file mode 100644 index 0000000..5078c69 --- /dev/null +++ b/examples/appletParameters.html @@ -0,0 +1,294 @@ + +Applet Parameters +
       
+

Download the applet jar file from here. Parameters are described + below, and the javascript API is described here. +

+

Useful to know!!

+
    +
  • 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
    + <applet code="jalview.bin.JalviewLite" + archive="jalviewApplet.jar, mydata.zip">
    +
    • +
  • Use Jalview for input to a HTML form. For an example of how to + code this using Javascript, click here. +
    +
    • +
  • Embed Jalview into the web page, without the "Start Jalview" + button by setting the embed parameter to true;
    + <param name="embedded" + value="true">
    • +

**NEW FEATURES** in Jalview 2.6

  • Jmol compatibility updated to Jmol 12.1.x series - download the JmolApplet here
  • To use Jmol as the structure viewer for Jalview, you must include the jar file in the applet archive argument thus:
    archive="jalviewApplet.jar,Jmol-12.1.13.jar"
  • Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the original Jalview structure viewer will still be available.
  • 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 download the Jmol applet from here
  • 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).
+
**NEW FEATURES** in Jalview 2.5

  • New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.

**NEW FEATURES** in Jalview 2.4

+
    +
  • New applet API methods for feature display control, views, and obtaining current selection via javascript.
    • +
  • 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. +
    • +
  • Regular expressions can be used in URL links for sequence IDs.
    • +
  • "debug" parameter to control verbosity of the applet's console output.
    • +
  • "showbutton" parameter to disable launch button and open JalviewLite immediatly.
    • +
  • "nojmol" parameter to disable check for Jmol classes.
    • +

+ **NEW FEATURES** in Jalview 2.3

+
    +
  • 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:
    +
    + <param name="PDBFile" value="First.pdb SeqA SeqB + SeqC">
    + <param name="PDBFile2" value="Second.pdb + A=SeqA B=SeqB C=SeqC">
    + <param name="PDBFile3" value="Third.pdb + D=SeqX B=SeqY C=SeqZ">
    +
    • +
  • Note parameter "PDBSeq" is no longer required.
    +
    • +
  • Jalview 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.
    • +

     

    + +
+ **NEW FEATURES** in Jalview 2.1 +
    +
  • Jalview Applet can read and display JNet secondary structure annotation + directly via the jnetfile parameter.
    +
    • +
  • 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:
    + <param name="userDefinedColour" + value="D,E=red; K,R,H=0022FF; C=yellow">
    +
    • +
  • Param showFeatureSettings + - this will display the feature settings window when the applet starts.
    +
    • +
  • Param Application_URL value="http://www.jalview.org/services/launchApp"
    +     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.
    +
    • +
  • Alignment file can be a series of parameters using eg PFAM format +
    + <param name="sequence1" + value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI">
    + <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT">
    +     (All the usual Jalview File formats are valid, however each + new line in an alignment file must be entered as a parameter)
    +
    • +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
<param name=""value="">Description
filefileNameThe file to open, must be on same server as the applet.
sequence1,
+ sequence2,
+ sequence3		sequence in (preferably) PFAM or Fasta formatThe alignment can be added as a series of sequences instead of + from a file.
treefileNameTree file in Newick format
featuresfileNameJalview Features file to be applied to the alignment
annotationsfileNameJalview Annotation file will be added to the alignment
jnetfilefileNameSecondary structure predictions from a Jnet Concise + file will be added to the first sequence in the alignment.
PDBfile(x)

fileName seq1 seq2 seq3

+

or

+

fileName A=seq1 B=seq2 C=seq3

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

PDBSeq
+ *Not needed post Jalview 2.3, use PDBFile instead

SequenceIdThe sequence to associate a PDB file with. Note the value is case + sensitive.
defaultColour One of:
+ Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix + Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide		Default is no colour.
userDefinedColour

Example:
+ D,E=red; K,R,H=0022FF; c=yellow

Define residue colours
showFullIdtrue or falseif true displays start and end residue at the end of sequence + Id.
showAnnotationtrue or falseIf true shows the annotation panel below the alignment.
showConservationtrue or falseDefault is true.
showQualitytrue or falseDefault is true.
showConsensustrue or falseDefault is true.
sortBy Id , Pairwise Identity, or Length Sorts the alignment on startup
RGBcolour as hex stringBackground colour for applet button - purely cosmetic to blend + in with your web page. For orange, enter the value FF6600
embeddedtrue or falseThe applet is embedded in the web page, the "Start Jalview" + button is not displayed.
windowWidthvalueframe width
windowHeightvalueframe height
labellabel textChange text for the Launch Jalview Button
wraptrue or falseOpens new windows in wrapped mode
linkLabel_1Uniprot

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
+ <param name="linkLabel_2" ...,
+ <param name="linkUrl_2"....
+

+

Regular expressions may also be used (since Jalview 2.4) to process the ID string inserted into the URL: +
$SEQUENCE_ID=/<regex to extract ID>/=$
Use the debug flag to check parsing and make sure that special symbols are properly escaped (particularly when generating applet tags from CGI scripts). +
Regex URL links are also applied to the description line (since Jalview 2.4.+).


+ linkUrl_1
+


+ http://us.expasy.org/cgi-bin/
+ niceprot.pl?$SEQUENCE_ID$

+
showFeatureSettingstrue or falseShows the feature settings window when starting the applet
showfeaturegroupsseparator separated list of feature groupsDisplay the features in the given groups on the alignment
hidefeaturegroupsseparator separated list of feature groupsHide the features in the given groups on the alignment + (will be overridden by showfeaturegroups for group names + found in both lists)
application_url

URL of dynamic JNLP servlet,

+

http://www.jalview.org/services/launchApp

Launches full application with original alignment, features and + annotations files used in applet
separatornon-empty separator string
default: |		string used to separate fields in list parameters (such as showfeaturegroups)
debugtrueInstruct the applet to output additional debug messages to the java console
nojmolfalseWhen 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. +
showbuttontrueShow the jalview button on the page. When false, JalviewLite will open immediately.
sortByTree true or false (default is false) automatically sort the associated alignment view by the tree when a new tree is opened.
showTreeBootstrapstrue or false (default is true)show or hide branch bootstraps
showTreeDistancestrue or false (default is true)show or hide branch lengths
showUnlinkedTreeNodestrue or false (default is false)indicate if unassociated nodes should be highlighted in the tree view
heightScale 1.0 or greater Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.
widthScale 1.0 or greater Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.
+

 

+
\ No newline at end of file diff --git a/examples/applets.html b/examples/applets.html new file mode 100755 index 0000000..eeb0d87 --- /dev/null +++ b/examples/applets.html @@ -0,0 +1,137 @@ + +Jalview - Applets +
       
+

Jalview comes in two distinct flavours.
+
+ The main application allows connection to multiple web services provided + at the University of Dundee as well as a host of additional useful features + such as printing, making images from your alignment and annotating your + alignment. You need to download and install this software.

+

The applet version runs in web browsers and is a useful interactive + display for precalculated alignments, features and annotations files. + It does not have the full functionality of the main application, such + as making images, saving files, running web service jobs due to security + restrictions imposed on applets.

+

For more information on how to use the applet in your + website, see full list of applet + parameters.

+

Pressing one of the buttons below will load up a cut down version + of Jalview, which runs within your web browser.

+

Ferredoxins, chloroplast precursor related UniRef50 + cluster
+ (15 sequences x 150 residues)

+
+
+ + + + +
+ + + + +
+ + + + + + + + + + + User Defined Colours, loads an associated Newick + format tree file
+

 

+ + + + +
+ + + + +
+ + + + + + + + + + + + + + + Displays a features file on the alignment
+

 

+ + + + +
+ + + + +
+ + + + + + + + + + + + + + + Associates PDB file 1GAQ with sequence FER1_MAIZE
+

 

+ + + + +
+ + + + +
+ + + + + + + + + + + + + + + + + Displays a Multiple Sequence Alignment Based + JNet Prediction for a Sequence
+
+
\ No newline at end of file diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt new file mode 100755 index 0000000..dc1ba4d --- /dev/null +++ b/examples/exampleFeatures.txt @@ -0,0 +1,311 @@ +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 +Fer2 Status: True Positive Pfam 8_8 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 +Fer2 Status: True Positive Pfam 55_13 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 +Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam +Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath +Fer2 Status: True Positive Pfam 55_13 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 +Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam +Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath +Fer2 Status: True Positive Pfam 63_13 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 +Fer2 Status: True Positive Pfam 59_13 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 +Fer2 Status: True Positive Pfam 58_13 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 +Fer2 Status: True Positive Pfam 8_8 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 +Fer2 Status: True Positive Pfam 8_8 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 +Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam +Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath +Fer2 Status: True Positive Pfam 60_11 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 +Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam +Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath +Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam +Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath +ENDGROUP uniprot + + +STARTGROUP netphos +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_CAPAA -1 89 89 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 22_2 FER1_SOLLC -1 22 22 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER1_SOLLC -1 38 38 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 102_10 FER1_SOLLC -1 102 102 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 136_13 FER1_SOLLC -1 136 136 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 136_13 Q93XJ9_SOLTU -1 136 136 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 22_2 Q93XJ9_SOLTU -1 22 22 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 Q93XJ9_SOLTU -1 38 38 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 33_3 FER1_PEA -1 33 33 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 42_4 FER1_PEA -1 42 42 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_PEA -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_PEA -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 4_ FER1_PEA -1 4 4 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 28_2 FER1_PEA -1 28 28 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_PEA -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 117_11 Q7XA98_TRIPR -1 117 117 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 137_13 Q7XA98_TRIPR -1 137 137 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 144_14 Q7XA98_TRIPR -1 144 144 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 30_3 Q7XA98_TRIPR -1 30 30 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 31_3 Q7XA98_TRIPR -1 31 31 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 4_ Q7XA98_TRIPR -1 4 4 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 45_4 Q7XA98_TRIPR -1 45 45 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 46_4 Q7XA98_TRIPR -1 46 46 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 93_9 Q7XA98_TRIPR -1 93 93 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 88_8 FER1_SPIOL -1 88 88 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 112_11 FER1_SPIOL -1 112 112 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 139_13 FER1_SPIOL -1 139 139 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 73_7 FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER1_ARATH -1 19 19 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER1_ARATH -1 24 24 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_ARATH -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER1_ARATH -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_ARATH -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_ARATH -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER1_ARATH -1 75 75 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER_BRANA -1 38 38 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 62_6 FER_BRANA -1 62 62 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_BRANA -1 89 89 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 23_2 FER_BRANA -1 23 23 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 Q93Z60_ARATH -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 Q93Z60_ARATH -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 21_2 Q93Z60_ARATH -1 21 21 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 Q93Z60_ARATH -1 24 24 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 Q93Z60_ARATH -1 75 75 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 7_ FER1_MAIZE -1 7 7 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER1_MAIZE -1 19 19 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 44_4 FER1_MAIZE -1 44 44 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 45_4 FER1_MAIZE -1 45 45 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_MAIZE -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER1_MAIZE -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_MAIZE -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 134_13 FER1_MAIZE -1 134 134 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_MAIZE -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 115_11 FER1_MAIZE -1 115 115 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 133_13 O80429_MAIZE -1 133 133 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 82_8 O80429_MAIZE -1 82 82 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 9_ O80429_MAIZE -1 9 9 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 99_9 O80429_MAIZE -1 99 99 PHOSPHORYLATION (S) +ENDGROUP netphos + +STARTGROUP s3dm +Found in PDBs: 1a70.,1a70. ALPHA-BETA-MOTIF 115_11 FER1_SPIOL -1 115 119 ALPHA-BETA-MOTIF +Found in PDBs: 1a70. ASX-TURN-IIL 107_10 FER1_SPIOL -1 107 109 ASX-TURN-IIL +Found in PDBs: 1a70. ASX-TURN-IR 115_11 FER1_SPIOL -1 115 117 ASX-TURN-IR +Found in PDBs: 1a70. BETA-BULGE 102_10 FER1_SPIOL -1 102 103 BETA-BULGE +Found in PDBs: 1a70. BETA-TURN-IR 59_6 FER1_SPIOL -1 59 62 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 69_7 FER1_SPIOL -1 69 72 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 95_9 FER1_SPIOL -1 95 98 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 108_11 FER1_SPIOL -1 108 111 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 125_12 FER1_SPIOL -1 125 128 BETA-TURN-IR +Found in PDBs: 1a70. BETA-TURN-IR 141_14 FER1_SPIOL -1 141 144 BETA-TURN-IR +Found in PDBs: 1a70. NEST-LR 90_9 FER1_SPIOL -1 90 92 NEST-LR +Found in PDBs: 1a70. NEST-LR 92_9 FER1_SPIOL -1 92 94 NEST-LR +Found in PDBs: 1a70. NEST-LR 140_14 FER1_SPIOL -1 140 142 NEST-LR +Found in PDBs: 1a70. NEST-RL 81_8 FER1_SPIOL -1 81 83 NEST-RL +Found in PDBs: 1a70. NEST-RL 89_9 FER1_SPIOL -1 89 91 NEST-RL +Found in PDBs: 1a70. NEST-RL 91_9 FER1_SPIOL -1 91 93 NEST-RL +Found in PDBs: 1a70. NEST-RL 121_12 FER1_SPIOL -1 121 123 NEST-RL +Found in PDBs: 1a70. SCHELLMANN-LOOP-6 78_8 FER1_SPIOL -1 78 83 SCHELLMANN-LOOP-6 +Found in PDBs: 1a70. SCHELLMANN-LOOP-6 118_12 FER1_SPIOL -1 118 123 SCHELLMANN-LOOP-6 +Found in PDBs: 1a70. ST-MOTIF 59_6 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 +Found in PDBs: 1gaq.B ALPHA-BETA-MOTIF 76_8 FER1_MAIZE -1 76 80 ALPHA-BETA-MOTIF +Found in PDBs: 1gaq.B ALPHA-BETA-MOTIF 77_8 FER1_MAIZE -1 77 81 ALPHA-BETA-MOTIF +Found in PDBs: 1gaq.B BETA-TURN-IR 127_13 FER1_MAIZE -1 127 130 BETA-TURN-IR +Found in PDBs: 1gaq.B GAMMA-TURN-CLASSIC 113_11 FER1_MAIZE -1 113 115 GAMMA-TURN-CLASSIC +Found in PDBs: 1gaq.B GAMMA-TURN-INVERSE 59_6 FER1_MAIZE -1 59 61 GAMMA-TURN-INVERSE +Found in PDBs: 1gaq.B GAMMA-TURN-INVERSE 104_10 FER1_MAIZE -1 104 106 GAMMA-TURN-INVERSE +Found in PDBs: 1gaq.B NEST-LR 92_9 FER1_MAIZE -1 92 94 NEST-LR +Found in PDBs: 1gaq.B NEST-LR 94_9 FER1_MAIZE -1 94 96 NEST-LR +Found in PDBs: 1gaq.B NEST-RL 83_8 FER1_MAIZE -1 83 85 NEST-RL +Found in PDBs: 1gaq.B NEST-RL 91_9 FER1_MAIZE -1 91 93 NEST-RL +Found in PDBs: 1gaq.B NEST-RL 93_9 FER1_MAIZE -1 93 95 NEST-RL +Found in PDBs: 1gaq.B NEST-RL 123_12 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 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diff --git a/examples/ferredoxin.nw b/examples/ferredoxin.nw
new file mode 100755
index 0000000..d82ff48
--- /dev/null
+++ b/examples/ferredoxin.nw
@@ -0,0 +1 @@
+(((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);
diff --git a/examples/formComplete.html b/examples/formComplete.html
new file mode 100644
index 0000000..fb1d7de
--- /dev/null
+++ b/examples/formComplete.html
@@ -0,0 +1,304 @@
+
+
+
+
+JalviewLite Applet API and Form Complete Example
+ 
+
+
+ 
+
+
+
+
+
+
+
 
+  
+    
+      
+    
+  
       

+  
+     
+      
+      
+    
+  
 
+	  
+	  

+          
+             
+              
+            
+             
+              
+            
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+              
+            
+             
+              
+            
+             
+              
+            
+             
+              
+            
+             
+              
+            
+            
+              
+            
+             
+              
+            
+			 
+              
+            
+			 
+              
+            
+             
+              
+            
+            
+              
+            
+            
+            
+              
+            
+          
Home
Overview
Download
Applet 
+                Version
Screenshots
FAQ
Documentation
Release 
+                history
Source 
+                Code
Development Version
Links
News 
+                Mailing List
Discussion Mailing List

Please send problems
and
+            bug reports to the discussion list.

+        

+        
 

+           
+        

+        		
+		
 

+		Click the Javascript buttons below to interact with the Applet
+		instance on the page.

+		View the source in your browser to see how it has been done.

+		The applet's public API methods are listed below
+		the following example.

+		
+			
+			
+			
+			
+			
+			
+			
+			
+			
+			
+			
+			
+			
+			
+		
+		


+		

+		
Using the Jalview Applet for Input
+		to an HTML Form

+		
 

+		

+		

+		

+		
Make a new View and Get and Set
+		Group Display List

+		

+		
  

+		 

+		 

+		

+		
 Since Jalview 2.5, the public methods listed
+		below are available to be called via Javascript.

+		
Unfortunately Javascript - Java communication is not possible
+		using Internet Explorer or Opera on Macs. Please use Safari or
+		Firefox.

+		
If more than one Jalview window is open, Jalview returns the
+		alignment in the active window, unless you provide an AlignFrame
+		object reference.

+		
The alignment output format can be either Fasta, PFAM, Clustal,
+		MSF, PIR, or BLC.

+		
When referring to the Jalview applet in javascript, you must
+		either give Jalview a name in the applet tag or use the applets index.

+
+		
//get list of IDs of selected sequences
+public String getSelectedSequences()
+
+// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (&#172;)
+public String getSelectedSequences(sep)
+
+// get selected sequences as alignment as format with or without start-end suffix
+public String getSelectedSequencesAsAlignment(String format, boolean suffix)
+
+// get selected sequences as alignment from given view as format with or without start-end suffix
+public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix)
+
+// get alignment as format
+public String getAlignment(String format)
+
+// get alignment as format with jalview 
+// start-end sequence suffix appended
+public String getAlignment(String format, String suffix)
+
+// get alignment displayed in alf as format
+public String getAlignmentFrom(AlignFrame alf, String format)
+
+// get alignment displayed in alf as format 
+// with jalview start-end sequence suffix appended
+public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
+
+// add the given features or annotation to the current alignment
+public void loadAnnotation(String annotation)
+
+// add the given features or annotation to the given alignment view
+public void loadAnnotationFrom(AlignFrame alf, String annotation)
+
+// get the sequence features in the given format (Jalview or GFF)
+public String getFeatures(String format)
+
+// get the sequence features in alf in the given format (Jalview or GFF)
+public String getFeaturesFrom(AlignFrame alf, String format)
+
+// get current alignment's annotation as an annotation file
+public String getAnnotation()
+
+// get alignment view alf's annotation as an annotation file
+public String getAnnotationFrom(AlignFrame alf)
+
+// create a new view and return the alignFrame instance
+public AlignFrame newView()
+
+// create a new view named name and return the alignFrame instance
+public AlignFrame newView(String name)
+
+// create a new view on alf and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf)
+
+// create a new view named name on alf 
+// and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf, String name)
+
+// load a new alignment 
+public AlignFrame loadAlignment(String text, String title)
+
+// return separator separated list of feature groups 
+// on the current alignment
+public String getFeatureGroups()
+
+// return separator separated list of feature groups on alf
+public String getFeatureGroupsOn(AlignFrame alf)
+
+// return separator separated list of feature groups 
+// either visible or hidden
+public String getFeatureGroupsOfState(boolean state)
+
+// return separator separated list of feature groups 
+// either visible or hidden on alf
+public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state)
+
+// set the separator separated list of feature groups as 
+// visible or hidden on the current alignment
+public void setFeatureGroupState(String groupList, boolean state)
+
+// set the separator separated list of feature groups 
+// as visible or hidden on alf
+public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state)
+
+// helper functions
+
+// convert list to a separator separated array
+public String arrayToSeparatorList(String[] list) 
+
+// get a string array from a list
+public String[] separatorListToArray(String list)
+
+// get the current separator
+public String getSeparator()
+
+// set the current separator
+public void setSeparator(String)
+
+//// JalviewLite global state methods and fields
+
+// return the build date as a string
+public static String getBuildDate() 
+
+// return the JalviewLite version as a string
+public static String getVersion()
+
+// debug flag - controls output to standard out
+public static boolean debug
+
+
 

+

+
+
diff --git a/examples/globins.jar b/examples/globins.jar
new file mode 100755
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z?l(-~l5W(^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-
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+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--
diff --git a/examples/jpred_msa.seq.concise b/examples/jpred_msa.seq.concise
new file mode 100755
index 0000000..90bd4c3
--- /dev/null
+++ b/examples/jpred_msa.seq.concise
@@ -0,0 +1,30 @@
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+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,-,
diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa
new file mode 100644
index 0000000..1412a5a
--- /dev/null
+++ b/examples/plantfdx.fa
@@ -0,0 +1,60 @@
+>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--
diff --git a/examples/plantfdx.features b/examples/plantfdx.features
new file mode 100644
index 0000000..eb5f0d3
--- /dev/null
+++ b/examples/plantfdx.features
@@ -0,0 +1,118 @@
+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
+Description: Fer2 Status: True Positive Pfam 8_83	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
+Description: Fer2 Status: True Positive Pfam 55_130	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
+Description: Fer2 Status: True Positive Pfam 55_130	FER1_SOLLC	-1	55	130	Pfam
+Evidence: EI4 	Q93XJ9_SOLTU	-1	1	48	SIGNAL
+Description: Fer2 Status: True Positive Pfam 55_130	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
+Description: Fer2 Status: True Positive Pfam 60_135	FER1_PEA	-1	60	135	Pfam
+Description: Fer2 Status: True Positive Pfam 63_138	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
+Description: Fer2 Status: True Positive Pfam 59_134	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
+Description: Fer2 Status: True Positive Pfam 58_133	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
+Description: Fer2 Status: True Positive Pfam 8_83	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
+Description: Fer2 Status: True Positive Pfam 60_135	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
+Description: Fer2 Status: True Positive Pfam 8_83	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
+Description: Fer2 Status: True Positive Pfam 60_135	FER2_ARATH	-1	60	135	Pfam
+Description: Fer2 Status: True Positive Pfam 60_118	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
+Description: Fer2 Status: True Positive Pfam 60_135	FER1_MAIZE	-1	60	135	Pfam
+Description: Fer2 Status: True Positive Pfam 52_127	O80429_MAIZE	-1	52	127	Pfam
+ENDGROUP	uniprot
diff --git a/examples/uniref50.fa b/examples/uniref50.fa
new file mode 100755
index 0000000..53698a4
--- /dev/null
+++ b/examples/uniref50.fa
@@ -0,0 +1,60 @@
+>FER_CAPAA Ferredoxin
+-----------------------------------------------------------ASYKVKLITPDGP
+IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV
+TIETHKEAELVG-
+>FER_CAPAN Ferredoxin, chloroplast precursor
+MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP
+IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV
+TIETHKEAELVG-
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor
+MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV
+TIETHKEEELTA-
+>Q93XJ9_SOLTU Ferredoxin I precursor
+MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV
+TIETHKEEELTA-
+>FER1_PEA Ferredoxin-1, chloroplast precursor
+MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT
+QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV
+VIETHKEEDLTA-
+>Q7XA98_TRIPR Ferredoxin I
+MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP
+QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV
+TIETHKEEELTA-
+>FER1_MESCR Ferredoxin-1, chloroplast precursor
+MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK
+QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV
+TIETHKEEELTA-
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor
+MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN
+VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV
+TIETHKEEELTA-
+>FER3_RAPSA Ferredoxin, leaf L-A
+-----------------------------------------------------------ATYKVKFITPEGE
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
+TIETHREEDMV--
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
+TIETHKEEDIV--
+>FER_BRANA Ferredoxin
+-----------------------------------------------------------ATYKVKFITPEGE
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
+TIETHKEEELV--
+>FER2_ARATH Ferredoxin-2, chloroplast precursor
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
+VIETHKEEAIM--
+>Q93Z60_ARATH At1g10960/T19D16_12
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------
+-------------
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor
+MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE
+VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV
+VIETHKEEELTGA
+>O80429_MAIZE Ferredoxin
+MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE
+VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV
+VIETHKEDDLL--
-- 
1.7.10.2