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adding jaxbtest.jvx and directing JalviewJS2.java to open it.
authorhansonr <hansonr@STO24954W.ad.stolaf.edu>
Sat, 1 Dec 2018 11:44:39 +0000 (05:44 -0600)
committerhansonr <hansonr@STO24954W.ad.stolaf.edu>
Sat, 1 Dec 2018 11:44:39 +0000 (05:44 -0600)
examples/jaxbtest.jvx [new file with mode: 0644] patch | blob
site-resources/examples/exampleFeatures.txt [new file with mode: 0644] patch | blob
site-resources/examples/jaxbtest.jvx [new file with mode: 0644] patch | blob
site-resources/examples/uniref50.fa [new file with mode: 0644] patch | blob
src/jalview/bin/JalviewJS2.java patch | blob | history

diff --git a/examples/jaxbtest.jvx b/examples/jaxbtest.jvx
new file mode 100644 (file)
index 0000000..5720bd0
Binary files /dev/null and b/examples/jaxbtest.jvx differ
diff --git a/site-resources/examples/exampleFeatures.txt b/site-resources/examples/exampleFeatures.txt
new file mode 100644 (file)
index 0000000..99af214
--- /dev/null
+++ b/site-resources/examples/exampleFeatures.txt
@@ -0,0 +1,369 @@
+ST-TURN-IIL    blue
+GAMMA-TURN-CLASSIC     lightgray
+BETA-TURN-IR   9a6a94
+BETA-TURN-IL   d6a6ca
+BETA-BULGE     1dc451
+Pfam   dc206a
+PHOSPHORYLATION (S)    b974a5
+PHOSPHORYLATION (Y)    7d3881
+Cath   93b1d1
+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
+kdHydrophobicity       ccffcc|333300|-3.9|4.5|above|-2.0
+
+STARTFILTERS
+GAMMA-TURN-INVERSE     Label Contains PDB
+kdHydrophobicity       (Score LT 1.5) OR (Score GE 2.8)
+ENDFILTERS
+
+STARTGROUP     uniprot
+<html><a href="http://pfam.xfam.org/family/PF00111">Pfam family</a></html>     FER_CAPAA       -1      0       0       Pfam
+Iron-sulfur (2Fe-2S)   FER_CAPAA       -1      39      39      METAL
+Iron-sulfur (2Fe-2S)   FER_CAPAA       -1      44      44      METAL
+Iron-sulfur (2Fe-2S)   FER_CAPAA       -1      47      47      METAL
+Iron-sulfur (2Fe-2S)   FER_CAPAA       -1      77      77      METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     FER_CAPAA       -1      8       83      Pfam
+Ferredoxin_fold Status: True Positive  FER_CAPAA       -1      3       93      Cath
+Iron-sulfur (2Fe-2S)   FER_CAPAN       -1      86      86      METAL
+Iron-sulfur (2Fe-2S)   FER_CAPAN       -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER_CAPAN       -1      94      94      METAL
+Iron-sulfur (2Fe-2S)   FER_CAPAN       -1      124     124     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html>   FER_CAPAN       -1      55      130     Pfam
+Ferredoxin_fold Status: True Positive  FER_CAPAN       -1      45      140     Cath
+Iron-sulfur (2Fe-2S)   FER1_SOLLC      -1      86      86      METAL
+Iron-sulfur (2Fe-2S)   FER1_SOLLC      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_SOLLC      -1      94      94      METAL
+Iron-sulfur (2Fe-2S)   FER1_SOLLC      -1      124     124     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html>   FER1_SOLLC      -1      55      130     Pfam
+Ferredoxin_fold Status: True Positive  FER1_SOLLC      -1      45      140     Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html>   Q93XJ9_SOLTU    -1      55      130     Pfam
+Ferredoxin_fold Status: True Positive  Q93XJ9_SOLTU    -1      45      140     Cath
+Iron-sulfur (2Fe-2S)   FER1_PEA        -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_PEA        -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_PEA        -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_PEA        -1      129     129     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER1_PEA        -1      60      135     Pfam
+Ferredoxin_fold Status: True Positive  FER1_PEA        -1      50      145     Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 63_13</a></html>   Q7XA98_TRIPR    -1      63      138     Pfam
+Ferredoxin_fold Status: True Positive  Q7XA98_TRIPR    -1      53      148     Cath
+Iron-sulfur (2Fe-2S)   FER1_MESCR      -1      90      90      METAL
+Iron-sulfur (2Fe-2S)   FER1_MESCR      -1      95      95      METAL
+Iron-sulfur (2Fe-2S)   FER1_MESCR      -1      98      98      METAL
+Iron-sulfur (2Fe-2S)   FER1_MESCR      -1      128     128     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 59_13</a></html>   FER1_MESCR      -1      59      134     Pfam
+Ferredoxin_fold Status: True Positive  FER1_MESCR      -1      49      144     Cath
+Iron-sulfur (2Fe-2S)   FER1_SPIOL      -1      89      89      METAL
+Iron-sulfur (2Fe-2S)   FER1_SPIOL      -1      94      94      METAL
+Iron-sulfur (2Fe-2S)   FER1_SPIOL      -1      97      97      METAL
+Iron-sulfur (2Fe-2S)   FER1_SPIOL      -1      127     127     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 58_13</a></html>   FER1_SPIOL      -1      58      133     Pfam
+Ferredoxin_fold Status: True Positive  FER1_SPIOL      -1      48      143     Cath
+Iron-sulfur (2Fe-2S)   FER3_RAPSA      -1      39      39      METAL
+Iron-sulfur (2Fe-2S)   FER3_RAPSA      -1      44      44      METAL
+Iron-sulfur (2Fe-2S)   FER3_RAPSA      -1      47      47      METAL
+Iron-sulfur (2Fe-2S)   FER3_RAPSA      -1      77      77      METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     FER3_RAPSA      -1      8       83      Pfam
+Ferredoxin_fold Status: True Positive  FER3_RAPSA      -1      3       93      Cath
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      39      39      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      44      44      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      47      47      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     FER_BRANA       -1      8       83      Pfam
+Ferredoxin_fold Status: True Positive  FER_BRANA       -1      2       96      Cath
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER1_ARATH      -1      60      135     Pfam
+Ferredoxin_fold Status: True Positive  FER1_ARATH      -1      50      145     Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_11</a></html>   Q93Z60_ARATH    -1      60      118     Pfam
+Ferredoxin_fold Status: True Positive  Q93Z60_ARATH    -1      52      118     Cath
+Iron-sulfur (2Fe-2S)   FER1_MAIZE      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_MAIZE      -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_MAIZE      -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_MAIZE      -1      129     129     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER1_MAIZE      -1      60      135     Pfam
+Ferredoxin_fold Status: True Positive  FER1_MAIZE      -1      50      145     Cath
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 52_12</a></html>   O80429_MAIZE    -1      52      127     Pfam
+Ferredoxin_fold Status: True Positive  O80429_MAIZE    -1      42      137     Cath
+ENDGROUP       uniprot
+
+
+STARTGROUP     netphos
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html>       FER_CAPAA       -1      89      89      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html>       FER1_SOLLC      -1      22      22      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html>       FER1_SOLLC      -1      38      38      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 102_10</a></html>     FER1_SOLLC      -1      102     102     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html>     FER1_SOLLC      -1      136     136     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html>     Q93XJ9_SOLTU    -1      136     136     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html>       Q93XJ9_SOLTU    -1      22      22      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html>       Q93XJ9_SOLTU    -1      38      38      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 33_3</a></html>       FER1_PEA        -1      33      33      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 42_4</a></html>       FER1_PEA        -1      42      42      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>       FER1_PEA        -1      90      90      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html>     FER1_PEA        -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> FER1_PEA        -1      4       4       PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 28_2</a></html>       FER1_PEA        -1      28      28      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html>     FER1_PEA        -1      141     141     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 117_11</a></html>     Q7XA98_TRIPR    -1      117     117     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 137_13</a></html>     Q7XA98_TRIPR    -1      137     137     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 144_14</a></html>     Q7XA98_TRIPR    -1      144     144     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 30_3</a></html>       Q7XA98_TRIPR    -1      30      30      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 31_3</a></html>       Q7XA98_TRIPR    -1      31      31      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> Q7XA98_TRIPR    -1      4       4       PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html>       Q7XA98_TRIPR    -1      45      45      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 46_4</a></html>       Q7XA98_TRIPR    -1      46      46      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 93_9</a></html>       Q7XA98_TRIPR    -1      93      93      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 88_8</a></html>       FER1_SPIOL      -1      88      88      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html>     FER1_SPIOL      -1      112     112     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html>     FER1_SPIOL      -1      139     139     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html>       FER1_SPIOL      -1      73      73      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER2_ARATH      -1      19      19      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER2_ARATH      -1      24      24      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER2_ARATH      -1      90      90      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER2_ARATH      -1      107     107     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER2_ARATH      -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER2_ARATH      -1      141     141     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER2_ARATH      -1      75      75      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html>       FER_BRANA       -1      38      38      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html>       FER_BRANA       -1      62      62      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html>       FER_BRANA       -1      89      89      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 23_2</a></html>       FER_BRANA       -1      23      23      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html>     Q93Z60_ARATH    -1      107     107     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html>     Q93Z60_ARATH    -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 21_2</a></html>       Q93Z60_ARATH    -1      21      21      PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>       Q93Z60_ARATH    -1      24      24      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>       Q93Z60_ARATH    -1      75      75      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 7_</a></html> FER1_MAIZE      -1      7       7       PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>       FER1_MAIZE      -1      19      19      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 44_4</a></html>       FER1_MAIZE      -1      44      44      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html>       FER1_MAIZE      -1      45      45      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>       FER1_MAIZE      -1      90      90      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html>     FER1_MAIZE      -1      107     107     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html>     FER1_MAIZE      -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 134_13</a></html>     FER1_MAIZE      -1      134     134     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html>     FER1_MAIZE      -1      141     141     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 115_11</a></html>     FER1_MAIZE      -1      115     115     PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 133_13</a></html>     O80429_MAIZE    -1      133     133     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 82_8</a></html>       O80429_MAIZE    -1      82      82      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 9_</a></html> O80429_MAIZE    -1      9       9       PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 99_9</a></html>       O80429_MAIZE    -1      99      99      PHOSPHORYLATION (S)
+ENDGROUP       netphos
+
+STARTGROUP     s3dm
+<html>Found in PDBs: 1a70.,1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 115_11</a></html>  FER1_SPIOL      -1      115     119     ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturniil?gzip=false">ASX-TURN-IIL 107_10</a></html>        FER1_SPIOL      -1      107     109     ASX-TURN-IIL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturnir?gzip=false">ASX-TURN-IR 115_11</a></html>  FER1_SPIOL      -1      115     117     ASX-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betabulge?gzip=false">BETA-BULGE 102_10</a></html>   FER1_SPIOL      -1      102     103     BETA-BULGE
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 59_6</a></html>  FER1_SPIOL      -1      59      62      BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 69_7</a></html>  FER1_SPIOL      -1      69      72      BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 95_9</a></html>  FER1_SPIOL      -1      95      98      BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 108_11</a></html>        FER1_SPIOL      -1      108     111     BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 125_12</a></html>        FER1_SPIOL      -1      125     128     BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 141_14</a></html>        FER1_SPIOL      -1      141     144     BETA-TURN-IR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 90_9</a></html>   FER1_SPIOL      -1      90      92      NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html>   FER1_SPIOL      -1      92      94      NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 140_14</a></html> FER1_SPIOL      -1      140     142     NEST-LR
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 81_8</a></html>   FER1_SPIOL      -1      81      83      NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 89_9</a></html>   FER1_SPIOL      -1      89      91      NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html>   FER1_SPIOL      -1      91      93      NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 121_12</a></html> FER1_SPIOL      -1      121     123     NEST-RL
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 78_8</a></html>        FER1_SPIOL      -1      78      83      SCHELLMANN-LOOP-6
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 118_12</a></html>      FER1_SPIOL      -1      118     123     SCHELLMANN-LOOP-6
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/stmotif?gzip=false">ST-MOTIF 59_6</a></html> FER1_SPIOL      -1      59      63      ST-MOTIF
+ALPHA-BETA-MOTIF       FER1_SPIOL      -1      65      69      ALPHA-BETA-MOTIF
+ASX-MOTIF      FER1_SPIOL      -1      65      69      ASX-MOTIF
+ASX-TURN-IIL   FER1_SPIOL      -1      57      59      ASX-TURN-IIL
+ASX-TURN-IR    FER1_SPIOL      -1      65      67      ASX-TURN-IR
+BETA-BULGE     FER1_SPIOL      -1      52      53      BETA-BULGE
+BETA-TURN-IR   FER1_SPIOL      -1      9       12      BETA-TURN-IR
+BETA-TURN-IR   FER1_SPIOL      -1      19      22      BETA-TURN-IR
+BETA-TURN-IR   FER1_SPIOL      -1      45      48      BETA-TURN-IR
+BETA-TURN-IR   FER1_SPIOL      -1      58      61      BETA-TURN-IR
+BETA-TURN-IR   FER1_SPIOL      -1      75      78      BETA-TURN-IR
+BETA-TURN-IR   FER1_SPIOL      -1      91      94      BETA-TURN-IR
+NEST-LR        FER1_SPIOL      -1      40      42      NEST-LR
+NEST-LR        FER1_SPIOL      -1      42      44      NEST-LR
+NEST-LR        FER1_SPIOL      -1      90      92      NEST-LR
+NEST-RL        FER1_SPIOL      -1      31      33      NEST-RL
+NEST-RL        FER1_SPIOL      -1      39      41      NEST-RL
+NEST-RL        FER1_SPIOL      -1      41      43      NEST-RL
+NEST-RL        FER1_SPIOL      -1      71      73      NEST-RL
+SCHELLMANN-LOOP-6      FER1_SPIOL      -1      28      33      SCHELLMANN-LOOP-6
+SCHELLMANN-LOOP-6      FER1_SPIOL      -1      68      73      SCHELLMANN-LOOP-6
+ST-MOTIF       FER1_SPIOL      -1      9       13      ST-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 76_8</a></html> FER1_MAIZE      -1      76      80      ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 77_8</a></html> FER1_MAIZE      -1      77      81      ALPHA-BETA-MOTIF
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 127_13</a></html>       FER1_MAIZE      -1      127     130     BETA-TURN-IR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturnclassic?gzip=false">GAMMA-TURN-CLASSIC 113_11</a></html>   FER1_MAIZE      -1      113     115     GAMMA-TURN-CLASSIC
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 59_6</a></html>     FER1_MAIZE      -1      59      61      GAMMA-TURN-INVERSE
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 104_10</a></html>   FER1_MAIZE      -1      104     106     GAMMA-TURN-INVERSE
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html>  FER1_MAIZE      -1      92      94      NEST-LR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 94_9</a></html>  FER1_MAIZE      -1      94      96      NEST-LR
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 83_8</a></html>  FER1_MAIZE      -1      83      85      NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html>  FER1_MAIZE      -1      91      93      NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 93_9</a></html>  FER1_MAIZE      -1      93      95      NEST-RL
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 123_12</a></html>        FER1_MAIZE      -1      123     125     NEST-RL
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      132     136     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      174     178     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      175     179     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      180     184     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      181     185     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      214     218     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      215     219     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      218     222     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      223     227     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      246     250     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      251     255     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      254     258     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      258     262     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      279     283     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      280     284     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      289     293     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      296     300     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      299     303     ALPHA-BETA-MOTIF
+ASX-TURN-IIL   FER1_MAIZE      -1      160     162     ASX-TURN-IIL
+ASX-TURN-IIR   FER1_MAIZE      -1      107     109     ASX-TURN-IIR
+BETA-BULGE     FER1_MAIZE      -1      31      32      BETA-BULGE
+BETA-BULGE     FER1_MAIZE      -1      43      44      BETA-BULGE
+BETA-TURN-IIL  FER1_MAIZE      -1      170     173     BETA-TURN-IIL
+BETA-TURN-IIR  FER1_MAIZE      -1      71      74      BETA-TURN-IIR
+BETA-TURN-IIR  FER1_MAIZE      -1      140     143     BETA-TURN-IIR
+BETA-TURN-IIR  FER1_MAIZE      -1      274     277     BETA-TURN-IIR
+BETA-TURN-IL   FER1_MAIZE      -1      64      67      BETA-TURN-IL
+BETA-TURN-IR   FER1_MAIZE      -1      33      36      BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      50      53      BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      100     103     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      103     106     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      136     139     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      171     174     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      172     175     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      206     209     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      207     210     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      223     226     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      233     236     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      252     255     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      264     267     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      289     292     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      295     298     BETA-TURN-IR
+CATMAT-3       FER1_MAIZE      -1      20      22      CATMAT-3
+CATMAT-3       FER1_MAIZE      -1      47      49      CATMAT-3
+CATMAT-3       FER1_MAIZE      -1      97      99      CATMAT-3
+CATMAT-4       FER1_MAIZE      -1      189     192     CATMAT-4
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      68      70      GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      84      86      GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      232     234     GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      240     242     GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      244     246     GAMMA-TURN-INVERSE
+NEST-LR        FER1_MAIZE      -1      30      32      NEST-LR
+NEST-LR        FER1_MAIZE      -1      66      68      NEST-LR
+NEST-LR        FER1_MAIZE      -1      106     108     NEST-LR
+NEST-LR        FER1_MAIZE      -1      108     110     NEST-LR
+NEST-LR        FER1_MAIZE      -1      212     214     NEST-LR
+NEST-LR        FER1_MAIZE      -1      276     278     NEST-LR
+NEST-LR        FER1_MAIZE      -1      307     309     NEST-LR
+NEST-RL        FER1_MAIZE      -1      64      66      NEST-RL
+NEST-RL        FER1_MAIZE      -1      105     107     NEST-RL
+NEST-RL        FER1_MAIZE      -1      107     109     NEST-RL
+NEST-RL        FER1_MAIZE      -1      306     308     NEST-RL
+ST-TURN-IIL    FER1_MAIZE      -1      20      22      ST-TURN-IIL
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      24      28      ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      25      29      ALPHA-BETA-MOTIF
+BETA-TURN-IR   FER1_MAIZE      -1      75      78      BETA-TURN-IR
+GAMMA-TURN-CLASSIC     FER1_MAIZE      -1      61      63      GAMMA-TURN-CLASSIC
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      7       9       GAMMA-TURN-INVERSE
+GAMMA-TURN-INVERSE     FER1_MAIZE      -1      52      54      GAMMA-TURN-INVERSE
+NEST-LR        FER1_MAIZE      -1      40      42      NEST-LR
+NEST-LR        FER1_MAIZE      -1      42      44      NEST-LR
+NEST-RL        FER1_MAIZE      -1      31      33      NEST-RL
+NEST-RL        FER1_MAIZE      -1      39      41      NEST-RL
+NEST-RL        FER1_MAIZE      -1      41      43      NEST-RL
+NEST-RL        FER1_MAIZE      -1      71      73      NEST-RL
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      176     180     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      233     237     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      247     251     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      278     282     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      286     290     ALPHA-BETA-MOTIF
+ALPHA-BETA-MOTIF       FER1_MAIZE      -1      295     299     ALPHA-BETA-MOTIF
+ASX-MOTIF      FER1_MAIZE      -1      122     126     ASX-MOTIF
+ASX-MOTIF      FER1_MAIZE      -1      160     164     ASX-MOTIF
+ASX-TURN-IR    FER1_MAIZE      -1      122     124     ASX-TURN-IR
+BETA-BULGE-LOOP-5      FER1_MAIZE      -1      122     126     BETA-BULGE-LOOP-5
+BETA-BULGE-LOOP-5      FER1_MAIZE      -1      239     243     BETA-BULGE-LOOP-5
+BETA-TURN-IR   FER1_MAIZE      -1      122     125     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      160     163     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      239     242     BETA-TURN-IR
+BETA-TURN-IR   FER1_MAIZE      -1      261     264     BETA-TURN-IR
+CATMAT-3       FER1_MAIZE      -1      80      82      CATMAT-3
+CATMAT-3       FER1_MAIZE      -1      87      89      CATMAT-3
+CATMAT-3       FER1_MAIZE      -1      262     264     CATMAT-3
+NEST-RL        FER1_MAIZE      -1      124     126     NEST-RL
+NEST-RL        FER1_MAIZE      -1      241     243     NEST-RL
+NEST-RL        FER1_MAIZE      -1      292     294     NEST-RL
+ENDGROUP       s3dm
+
+STARTGROUP     kd
+A      Q93XJ9_SOLTU    -1      48      48      kdHydrophobicity        1.8
+A      Q93XJ9_SOLTU    -1      49      49      kdHydrophobicity        -0.8
+A      Q93XJ9_SOLTU    -1      50      50      kdHydrophobicity        -1.3
+A      Q93XJ9_SOLTU    -1      51      51      kdHydrophobicity        -3.9
+A      Q93XJ9_SOLTU    -1      52      52      kdHydrophobicity        4.2
+A      Q93XJ9_SOLTU    -1      53      53      kdHydrophobicity        -3.9
+A      Q93XJ9_SOLTU    -1      54      54      kdHydrophobicity        3.8
+A      Q93XJ9_SOLTU    -1      55      55      kdHydrophobicity        4.5
+A      Q93XJ9_SOLTU    -1      56      56      kdHydrophobicity        -0.7
+A      Q93XJ9_SOLTU    -1      57      57      kdHydrophobicity        -1.6
+A      Q93XJ9_SOLTU    -1      58      58      kdHydrophobicity        -3.5
+A      Q93XJ9_SOLTU    -1      59      59      kdHydrophobicity        -0.4
+A      Q93XJ9_SOLTU    -1      60      60      kdHydrophobicity        -1.6
+A      Q93XJ9_SOLTU    -1      61      61      kdHydrophobicity        4.5
+A      Q93XJ9_SOLTU    -1      62      62      kdHydrophobicity        -3.5
+A      Q93XJ9_SOLTU    -1      63      63      kdHydrophobicity        2.8
+A      FER1_SPIOL      -1      51      51      kdHydrophobicity        1.8
+A      FER1_SPIOL      -1      52      52      kdHydrophobicity        1.8
+A      FER1_SPIOL      -1      53      53      kdHydrophobicity        -1.3
+A      FER1_SPIOL      -1      54      54      kdHydrophobicity        -3.9
+A      FER1_SPIOL      -1      55      55      kdHydrophobicity        4.2
+A      FER1_SPIOL      -1      56      56      kdHydrophobicity        -0.7
+A      FER1_SPIOL      -1      57      57      kdHydrophobicity        3.8
+A      FER1_SPIOL      -1      58      58      kdHydrophobicity        4.2
+A      FER1_SPIOL      -1      59      59      kdHydrophobicity        -0.7
+A      FER1_SPIOL      -1      60      60      kdHydrophobicity        -1.6
+A      FER1_SPIOL      -1      61      61      kdHydrophobicity        -0.7
+A      FER1_SPIOL      -1      62      62      kdHydrophobicity        -0.4
+A      FER1_SPIOL      -1      63      63      kdHydrophobicity        -3.5
+A      FER1_SPIOL      -1      64      64      kdHydrophobicity        4.2
+A      FER1_SPIOL      -1      65      65      kdHydrophobicity        -3.5
+A      FER1_SPIOL      -1      66      66      kdHydrophobicity        2.8
+C      FER1_MAIZE      -1      53      53      kdHydrophobicity        1.8
+C      FER1_MAIZE      -1      54      54      kdHydrophobicity        -0.7
+C      FER1_MAIZE      -1      55      55      kdHydrophobicity        -1.3
+C      FER1_MAIZE      -1      56      56      kdHydrophobicity        -3.5
+C      FER1_MAIZE      -1      57      57      kdHydrophobicity        4.2
+C      FER1_MAIZE      -1      58      58      kdHydrophobicity        -3.9
+C      FER1_MAIZE      -1      59      59      kdHydrophobicity        3.8
+C      FER1_MAIZE      -1      60      60      kdHydrophobicity        4.5
+C      FER1_MAIZE      -1      61      61      kdHydrophobicity        -0.7
+C      FER1_MAIZE      -1      62      62      kdHydrophobicity        -1.6
+C      FER1_MAIZE      -1      63      63      kdHydrophobicity        -3.5
+C      FER1_MAIZE      -1      64      64      kdHydrophobicity        -0.4
+C      FER1_MAIZE      -1      65      65      kdHydrophobicity        -3.5
+C      FER1_MAIZE      -1      66      66      kdHydrophobicity        4.2
+C      FER1_MAIZE      -1      67      67      kdHydrophobicity        -3.5
+C      FER1_MAIZE      -1      68      68      kdHydrophobicity        3.8
+ENDGROUP       kd
diff --git a/site-resources/examples/jaxbtest.jvx b/site-resources/examples/jaxbtest.jvx
new file mode 100644 (file)
index 0000000..5720bd0
Binary files /dev/null and b/site-resources/examples/jaxbtest.jvx differ
diff --git a/site-resources/examples/uniref50.fa b/site-resources/examples/uniref50.fa
new file mode 100644 (file)
index 0000000..6e6c670
--- /dev/null
+++ b/site-resources/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--
+>FER2_ARATH Ferredoxin-2, chloroplast precursor
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
+TIETHKEEDIV--
+>FER_BRANA Ferredoxin
+-----------------------------------------------------------ATYKVKFITPEGE
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
+TIETHKEEELV--
+>FER1_ARATH Ferredoxin-1, 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--
diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java
index 037f41e..516cc20 100644 (file)
--- a/src/jalview/bin/JalviewJS2.java
+++ b/src/jalview/bin/JalviewJS2.java
@@ -13,13 +13,21 @@ public class JalviewJS2
 
   static {
     /**
-     * @j2sNative
+     * --j2sNative
      * 
      *            thisApplet.__Info.args =
-     *            ["open","http://www.jalview.org/builds/release/examples/uniref50.fa","features",
-     *            "http://www.jalview.org/builds/release/examples/exampleFeatures.txt"];
+     *            ["open","examples/uniref50.fa","features",
+     *            "examples/exampleFeatures.txt"];
      */
-    
+
+         
+           /**
+            * @j2sNative
+            * 
+            *            thisApplet.__Info.args =
+            *            ["open","examples/jaxbtest.jvx"];
+            */
+
   }
 
   public static void main(String[] args) throws Exception