ChimeraX-users July 2020

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42 discussions

color key
by Roberto Marabini 02 Jul '20

02 Jul '20

hi, Is there a colorkey command in chimeraX (http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…>)? If it does not exist, is there any alternative other than using chimera and photoshop? Thanks Roberto

3 3

Is color command slower in ChimeraX than Chimera?
by Mungo Carstairs (Staff) 30 Jun '20

30 Jun '20

Hi, I'm testing driving ChimeraX (or Chimera) from Jalview, in particular colouring structures using the Jalview alignment residue colouring. Ideally this should perform well at scale for large numbers of structures and/or colours (for example a graduated colouring based on some property). I've noticed that ChimeraX appears to do this slower than Chimera. Is there a reason, or something I should do to make the command faster? Here's an example like for like comparison using the Chimera/X command line (also attached as a text file): Chimera 1.15 (build 42156) > open cifID:4zho cifID:5h92 cifID:1a70 cifID:4zhp > focus > color #977b64 #0:2.A,2.B;color #e46daf #0:3.A,3.B;color #7dc891 #0:4.A,4.B;color #768daf #0:5.A,5.B;color #bb1691 #0:6.A,6.B;color #1c5355 #0:7.A,7.B;color #5b1873 #0:8.A,8.B;color #d0af91 #0:9.A,9.B;color #6cb737 #0:10.A,10.B;color #8d7c55 #0:11.A,11.B;color #844173 #0:12.A,12.B;color #1f15a0 #0:13.A,13.B;color #a27f91 #0:14.A,14.B;color #19cb64 #0:15.A,15.B;color #484537 #0:16.A,16.B;color #61be37 #0:17.A,17.B;color #84a173 #0:18.A,18.B;color #c76691 #0:19.A,19.B;color #8f31a0 #0:20.A,20.B;color #9eb9af #0:21.A,21.B;color #531564 #0:22.A,22.B;color #707046 #0:23.A,23.B;color #9b80af #0:24.A,24.B;color #ca18a0 #0:25.A,25.B;color #377382 #0:26.A,26.B;color #26a137 #0:27.A,27.B;color #d3b1a0 #0:28.A,28.B;color #e267af #0:29.A,29.B;color #c023af #0:30.A,30.B;color #b18da0 #0:31.A,31.B;color #88bb55 #0:32.A,32.B;color #1fada0 #0:33.A,33.B;color #b22773 #0:34.A,34.B;color #ad19be #0:35.A,35.B;color #6483af #0:36.A,36.B;color #c9de91 #0:37.A,37.B;color #aab2be #0:38.A,38.B;color #59d164 #0:39.A,39.B;color #6d6037 #0:40.A,40.B;color #1cd937 #0:41.A,41.B;color #b5cb82 #0:42.A,42.B;color #e28191 #0:43.A,43.B;color #9537a0 #0:44.A,44.B;color #d6b0a0 #0:45.A,45.B;color #3bcf46 #0:46.A,46.B;color #2c6737 #0:47.A,47.B;color #e586af #0:48.A,48.B;color #e22daf #0:49.A,49.B;color #e29d91 #0:50.A,50.B;color #493582 #0:51.A,51.B;color #cacca0 #0:52.A,52.B;color #7f2855 #0:53.A,53.B;color #86dd91 #0:54.A,54.B;color #b55764 #0:55.A,55.B;color #4ac155 #0:56.A,56.B;color #614a37 #0:57.A,57.B;color #9e69af #0:58.A,58.B;color #5f8855 #0:59.A,59.B;color #958fa0 #0:60.A,60.B;color #9e45af #0:61.A,61.B;color #b9beaf #0:62.A,62.B;color #4add55 #0:63.A,63.B;color #5ba273 #0:64.A,64.B;color #bedf37 #0:65.A,65.B;color #359546 #0:66.A,66.B;color #262d37 #0:67.A,67.B;color #cf5bbe #0:68.A,68.B;color #505c46 #0:69.A,69.B;color #76db37 #0:70.A,70.B;color #3d37be #0:71.A,71.B;color #a28391 #0:72.A,72.B;color #b5cf64 #0:73.A,73.B;color #88b2a0 #0:74.A,74.B;color #bb4a91 #0:75.A,75.B;color #dc8755 #0:76.A,76.B;color #d579a0 #0:77.A,77.B;color #7c9846 #0:78.A,78.B;color #b57b82 #0:79.A,79.B;color #79cd46 #0:80.A,80.B;color #aa1abe #0:81.A,81.B;color #ab4873 #0:82.A,82.B;color #c6df91 #0:83.A,83.B;color #b3b3be #0:84.A,84.B;color #802d91 #0:85.A,85.B;color #d9c4af #0:86.A,86.B;color #c64d91 #0:87.A,87.B;color #857b46 #0:88.A,88.B;color #a26d91 #0:89.A,89.B;color #c62991 #0:90.A,90.B;color #adb1a0 #0:91.A,91.B;color #584991 #0:92.A,92.B;color #93b382 #0:93.A,93.B;color #48e137 #0:94.A,94.B;color #88c56f #1:1.C;color #7b5d60 #1:2.C;color #32d660 #1:3.C;color #339b7e #1:4.C;color #702460 #1:5.C;color #6725ba #1:6.C;color #dc536f #1:7.C;color #a3db7e #1:8.C;color #a8918d #1:9.C;color #d84eba #1:10.C;color #758b7e #1:11.C;color #88d751 #1:12.C;color #75ab7e #1:13.C;color #8e527e #1:14.C;color #cf53d8 #1:15.C;color #dc636f #1:16.C;color #7d288d #1:17.C;color #707460 #1:18.C;color #6fde51 #1:19.C;color #35a960 #1:20.C;color #627d8d #1:21.C;color #bb42ab #1:22.C;color #327060 #1:23.C;color #a3357e #1:24.C;color #28bd8d #1:25.C;color #8f91ba #1:26.C;color #c856d8 #1:27.C;color #795760 #1:28.C;color #c067c9 #1:29.C;color #669b6f #1:30.C;color #adabd8 #1:31.C;color #889d51 #1:32.C;color #c18f9c #1:33.C;color #26bd51 #1:34.C;color #55cdba #1:35.C;color #7e1a60 #1:36.C;color #238451 #1:37.C;color #68678d #1:38.C;color #6da451 #1:39.C;color #a315d8 #1:40.C;color #88256f #1:41.C;color #1f17ba #1:42.C;color #4a456f #1:43.C;color #6da051 #1:44.C;color #a4bfc9 #1:45.C;color #9557ba #1:46.C;color #d6d0ba #1:47.C;color #791d60 #1:48.C;color #e2e1ab #1:49.C;color #1c616f #1:50.C;color #7fda6f #1:51.C;color #8e907e #1:52.C;color #77559c #1:53.C;color #c4bf8d #1:54.C;color #77759c #1:55.C;color #1658d8 #1:56.C;color #add1d8 #1:57.C;color #aa5aba #1:58.C;color #95d3ba #1:59.C;color #adadd8 #1:60.C;color #aa36ba #1:61.C;color #95afba #1:62.C;color #aa74d8 #1:63.C;color #731bd8 #1:64.C;color #442b6f #1:65.C;color #8f1dba #1:66.C;color #882d51 #1:67.C;color #9b2eab #1:68.C;color #764d51 #1:69.C;color #6adb51 #1:70.C;color #359160 #1:71.C;color #e283ab #1:72.C;color #ddb160 #1:73.C;color #cab2ba #1:74.C;color #5559ba #1:75.C;color #8a876f #1:76.C;color #c76aab #1:77.C;color #62a76f #1:78.C;color #793f60 #1:79.C;color #23be51 #1:80.C;color #bab09c #1:81.C;color #99397e #1:82.C;color #a42bc9 #1:83.C;color #53597e #1:84.C;color #165ad8 #1:85.C;color #9d888d #1:86.C;color #d04dab #1:87.C;color #b1d5ba #1:88.C;color #c66dab #1:89.C;color #44a151 #1:90.C;color #df5760 #1:91.C;color #66df6f #1:92.C;color #cf1dd8 #1:93.C;color #a269ab #1:94.C;color #551fba #1:95.C;color #e4a7c9 #1:96.C;color #1f5c8b #2:1.A;color #a68a40 #2:2.A;color #5f3140 #2:3.A;color #76147c #2:4.A;color #9d5140 #2:5.A;color #6c8ed6 #2:6.A;color #37804f #2:7.A;color #8edb31 #2:8.A;color #7b64e5 #2:9.A;color #ab2140 #2:10.A;color #a89a40 #2:11.A;color #b53231 #2:12.A;color #7e247c #2:13.A;color #6125d6 #2:14.A;color #a2265e #2:15.A;color #97bd7c #2:16.A;color #aa556d #2:17.A;color #a9a140 #2:18.A;color #9c3931 #2:19.A;color #9e407c #2:20.A;color #8faa6d #2:21.A;color #166f8b #2:22.A;color #9bd97c #2:23.A;color #76dad6 #2:24.A;color #cd90e5 #2:25.A;color #2628d6 #2:26.A;color #97ce31 #2:27.A;color #e2c07c #2:28.A;color #933a4f #2:29.A;color #cf328b #2:30.A;color #a27e5e #2:31.A;color #b5ca31 #2:32.A;color #946222 #2:33.A;color #8f546d #2:34.A;color #28a040 #2:35.A;color #ab4740 #2:36.A;color #8c1b6d #2:37.A;color #95946d #2:38.A;color #d63b6d #2:39.A;color #76ba5e #2:40.A;color #b5524f #2:41.A;color #8880d6 #2:42.A;color #b3ae8b #2:43.A;color #9acd31 #2:44.A;color #77924f #2:45.A;color #2cc0d6 #2:46.A;color #a9a340 #2:47.A;color #e2867c #2:48.A;color #b5b431 #2:49.A;color #498e4f #2:50.A;color #64627c #2:51.A;color #85188b #2:52.A;color #e4827c #2:53.A;color #1f1a6d #2:54.A;color #a4a27c #2:55.A;color #cdb2e5 #2:56.A;color #60a45e #2:57.A;color #7d2d40 #2:58.A;color #80c45e #2:59.A;color #444422 #2:60.A;color #7ddb40 #2:61.A;color #688240 #2:62.A;color #1fbfd6 #2:63.A;color #46c05e #2:64.A;color #71584f #2:65.A;color #2686d6 #2:66.A;color #353ce5 #2:67.A;color #c85b8b #2:68.A;color #a37a31 #2:69.A;color #3518e5 #2:70.A;color #4882d6 #2:71.A;color #b55631 #2:72.A;color #74487c #2:73.A;color #6149d6 #2:74.A;color #282c40 #2:75.A;color #211e8b #2:76.A;color #22978b #2:77.A;color #7998e5 #2:78.A;color #a66c40 #2:79.A;color #501931 #2:80.A;color #15dd7c #2:81.A;color #ca756d #2:82.A;color #3b94e5 #2:83.A;color #262cd6 #2:84.A;color #7fc322 #2:85.A;color #a88840 #2:86.A;color #2b7a8b #2:87.A;color #486cd6 #2:88.A;color #994031 #2:89.A;color #71ce31 #2:90.A;color #3a8440 #2:91.A;color #ffffff #2:92.A;color #a2c25e #2:93.A;color #cf968b #2:94.A;color #28c440 #2:95.A;color #7b3ee5 #2:96.A;color #6aa8d6 #2:97.A;color #977b82 #3:2.A;color #683191 #3:3.A;color #7dc8af #3:4.A;color #768dcd #3:5.A;color #bb16af #3:6.A;color #1c5373 #3:7.A;color #3727a0 #3:8.A;color #d0afaf #3:9.A;color #6cb755 #3:10.A;color #8d7c73 #3:11.A;color #26d755 #3:12.A;color #1f15be #3:13.A;color #7e3464 #3:14.A;color #df35be #3:15.A;color #484555 #3:16.A;color #9764cd #3:17.A;color #84a191 #3:18.A;color #c766af #3:19.A;color #6f9a55 #3:20.A;color #9eb9cd #3:21.A;color #531582 #3:22.A;color #707064 #3:23.A;color #9b80cd #3:24.A;color #d0dbaf #3:25.A;color #3773a0 #3:26.A;color #26a155 #3:27.A;color #414855 #3:28.A;color #e267cd #3:29.A;color #c023cd #3:30.A;color #b18dbe #3:31.A;color #84d991 #3:32.A;color #1fadbe #3:33.A;color #bc63cd #3:34.A;color #ad19dc #3:35.A;color #6483cd #3:36.A;color #c9deaf #3:37.A;color #aab2dc #3:38.A;color #59d182 #3:39.A;color #6d6055 #3:40.A;color #1cd955 #3:41.A;color #b5cba0 #3:42.A;color #e281af #3:43.A;color #9537be #3:44.A;color #d6b0be #3:45.A;color #3bcf64 #3:46.A;color #2c6755 #3:47.A;color #e586cd #3:48.A;color #e22dcd #3:49.A;color #e29daf #3:50.A;color #4935a0 #3:51.A;color #caccbe #3:52.A;color #d573be #3:53.A;color #e229cd #3:54.A;color #b55782 #3:55.A;color #e449cd #3:56.A;color #614a55 #3:57.A;color #9e69cd #3:58.A;color #5f8873 #3:59.A;color #958fbe #3:60.A;color #9e45cd #3:61.A;color #975564 #3:62.A;color #1cdd73 #3:63.A;color #5ba291 #3:64.A;color #bedf55 #3:65.A;color #359564 #3:66.A;color #262d55 #3:67.A;color #711fa0 #3:68.A;color #505c64 #3:69.A;color #662773 #3:70.A;color #d319be #3:71.A;color #e2a1cd #3:72.A;color #b5cf82 #3:73.A;color #88b2be #3:74.A;color #bb4aaf #3:75.A;color #dc8773 #3:76.A;color #d579be #3:77.A;color #7c9864 #3:78.A;color #9d6c91 #3:79.A;color #79cd64 #3:80.A;color #aa1adc #3:81.A;color #ab4891 #3:82.A;color #1ca373 #3:83.A;color #8b4a73 #3:84.A;color #802daf #3:85.A;color #d9c4cd #3:86.A;color #c64daf #3:87.A;color #857b64 #3:88.A;color #a26daf #3:89.A;color #c629af #3:90.A;color #adb1be #3:91.A;color #5849af #3:92.A;color #93b3a0 #3:93.A;color #48e155 #3:94.A;color #93d3a0 #3:95.A;color #dc4d73 #3:96.A;color #d53fbe #3:97.A;color #6a4f55 #3:98.A On my Macbook these color commands take about 2 seconds. ChimeraX 1.0 (2020-06-04): > open pdb:4zho pdb:5h92 pdb:1a70 pdb:4zhp > view > color #1/A:2/B:2 #977b64;color #1/A:3/B:3 #e46daf;color #1/A:4/B:4 #7dc891;color #1/A:5/B:5 #768daf;color #1/A:6/B:6 #bb1691;color #1/A:7/B:7 #1c5355;color #1/A:8/B:8 #5b1873;color #1/A:9/B:9 #d0af91;color #1/A:10/B:10 #6cb737;color #1/A:11/B:11 #8d7c55;color #1/A:12/B:12 #844173;color #1/A:13/B:13 #1f15a0;color #1/A:14/B:14 #a27f91;color #1/A:15/B:15 #19cb64;color #1/A:16/B:16 #484537;color #1/A:17/B:17 #61be37;color #1/A:18/B:18 #84a173;color #1/A:19/B:19 #c76691;color #1/A:20/B:20 #8f31a0;color #1/A:21/B:21 #9eb9af;color #1/A:22/B:22 #531564;color #1/A:23/B:23 #707046;color #1/A:24/B:24 #9b80af;color #1/A:25/B:25 #ca18a0;color #1/A:26/B:26 #377382;color #1/A:27/B:27 #26a137;color #1/A:28/B:28 #d3b1a0;color #1/A:29/B:29 #e267af;color #1/A:30/B:30 #c023af;color #1/A:31/B:31 #b18da0;color #1/A:32/B:32 #88bb55;color #1/A:33/B:33 #1fada0;color #1/A:34/B:34 #b22773;color #1/A:35/B:35 #ad19be;color #1/A:36/B:36 #6483af;color #1/A:37/B:37 #c9de91;color #1/A:38/B:38 #aab2be;color #1/A:39/B:39 #59d164;color #1/A:40/B:40 #6d6037;color #1/A:41/B:41 #1cd937;color #1/A:42/B:42 #b5cb82;color #1/A:43/B:43 #e28191;color #1/A:44/B:44 #9537a0;color #1/A:45/B:45 #d6b0a0;color #1/A:46/B:46 #3bcf46;color #1/A:47/B:47 #2c6737;color #1/A:48/B:48 #e586af;color #1/A:49/B:49 #e22daf;color #1/A:50/B:50 #e29d91;color #1/A:51/B:51 #493582;color #1/A:52/B:52 #cacca0;color #1/A:53/B:53 #7f2855;color #1/A:54/B:54 #86dd91;color #1/A:55/B:55 #b55764;color #1/A:56/B:56 #4ac155;color #1/A:57/B:57 #614a37;color #1/A:58/B:58 #9e69af;color #1/A:59/B:59 #5f8855;color #1/A:60/B:60 #958fa0;color #1/A:61/B:61 #9e45af;color #1/A:62/B:62 #b9beaf;color #1/A:63/B:63 #4add55;color #1/A:64/B:64 #5ba273;color #1/A:65/B:65 #bedf37;color #1/A:66/B:66 #359546;color #1/A:67/B:67 #262d37;color #1/A:68/B:68 #cf5bbe;color #1/A:69/B:69 #505c46;color #1/A:70/B:70 #76db37;color #1/A:71/B:71 #3d37be;color #1/A:72/B:72 #a28391;color #1/A:73/B:73 #b5cf64;color #1/A:74/B:74 #88b2a0;color #1/A:75/B:75 #bb4a91;color #1/A:76/B:76 #dc8755;color #1/A:77/B:77 #d579a0;color #1/A:78/B:78 #7c9846;color #1/A:79/B:79 #b57b82;color #1/A:80/B:80 #79cd46;color #1/A:81/B:81 #aa1abe;color #1/A:82/B:82 #ab4873;color #1/A:83/B:83 #c6df91;color #1/A:84/B:84 #b3b3be;color #1/A:85/B:85 #802d91;color #1/A:86/B:86 #d9c4af;color #1/A:87/B:87 #c64d91;color #1/A:88/B:88 #857b46;color #1/A:89/B:89 #a26d91;color #1/A:90/B:90 #c62991;color #1/A:91/B:91 #adb1a0;color #1/A:92/B:92 #584991;color #1/A:93/B:93 #93b382;color #1/A:94/B:94 #48e137;color #2/C:1 #88c56f;color #2/C:2 #7b5d60;color #2/C:3 #32d660;color #2/C:4 #339b7e;color #2/C:5 #702460;color #2/C:6 #6725ba;color #2/C:7 #dc536f;color #2/C:8 #a3db7e;color #2/C:9 #a8918d;color #2/C:10 #d84eba;color #2/C:11 #758b7e;color #2/C:12 #88d751;color #2/C:13 #75ab7e;color #2/C:14 #8e527e;color #2/C:15 #cf53d8;color #2/C:16 #dc636f;color #2/C:17 #7d288d;color #2/C:18 #707460;color #2/C:19 #6fde51;color #2/C:20 #35a960;color #2/C:21 #627d8d;color #2/C:22 #bb42ab;color #2/C:23 #327060;color #2/C:24 #a3357e;color #2/C:25 #28bd8d;color #2/C:26 #8f91ba;color #2/C:27 #c856d8;color #2/C:28 #795760;color #2/C:29 #c067c9;color #2/C:30 #669b6f;color #2/C:31 #adabd8;color #2/C:32 #889d51;color #2/C:33 #c18f9c;color #2/C:34 #26bd51;color #2/C:35 #55cdba;color #2/C:36 #7e1a60;color #2/C:37 #238451;color #2/C:38 #68678d;color #2/C:39 #6da451;color #2/C:40 #a315d8;color #2/C:41 #88256f;color #2/C:42 #1f17ba;color #2/C:43 #4a456f;color #2/C:44 #6da051;color #2/C:45 #a4bfc9;color #2/C:46 #9557ba;color #2/C:47 #d6d0ba;color #2/C:48 #791d60;color #2/C:49 #e2e1ab;color #2/C:50 #1c616f;color #2/C:51 #7fda6f;color #2/C:52 #8e907e;color #2/C:53 #77559c;color #2/C:54 #c4bf8d;color #2/C:55 #77759c;color #2/C:56 #1658d8;color #2/C:57 #add1d8;color #2/C:58 #aa5aba;color #2/C:59 #95d3ba;color #2/C:60 #adadd8;color #2/C:61 #aa36ba;color #2/C:62 #95afba;color #2/C:63 #aa74d8;color #2/C:64 #731bd8;color #2/C:65 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#b55782;color #4/A:56 #e449cd;color #4/A:57 #614a55;color #4/A:58 #9e69cd;color #4/A:59 #5f8873;color #4/A:60 #958fbe;color #4/A:61 #9e45cd;color #4/A:62 #975564;color #4/A:63 #1cdd73;color #4/A:64 #5ba291;color #4/A:65 #bedf55;color #4/A:66 #359564;color #4/A:67 #262d55;color #4/A:68 #711fa0;color #4/A:69 #505c64;color #4/A:70 #662773;color #4/A:71 #d319be;color #4/A:72 #e2a1cd;color #4/A:73 #b5cf82;color #4/A:74 #88b2be;color #4/A:75 #bb4aaf;color #4/A:76 #dc8773;color #4/A:77 #d579be;color #4/A:78 #7c9864;color #4/A:79 #9d6c91;color #4/A:80 #79cd64;color #4/A:81 #aa1adc;color #4/A:82 #ab4891;color #4/A:83 #1ca373;color #4/A:84 #8b4a73;color #4/A:85 #802daf;color #4/A:86 #d9c4cd;color #4/A:87 #c64daf;color #4/A:88 #857b64;color #4/A:89 #a26daf;color #4/A:90 #c629af;color #4/A:91 #adb1be;color #4/A:92 #5849af;color #4/A:93 #93b3a0;color #4/A:94 #48e155;color #4/A:95 #93d3a0;color #4/A:96 #dc4d73;color #4/A:97 #d53fbe;color #4/A:98 #6a4f55 These color commands take 15-16 seconds. Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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