id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4509 Toolshed reporting obsolete command sergei.pourmal@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description Installed SEQCROW via ""toolshed install SEQCROW"" to run angle command. Seems to be installed per log. Run ""angle #2:281 #2:342 #2:916 short"" and receive the response ""angel is provided by the unstalled bundle SEQCROW"" Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210415.cxs format > session Log from Wed Apr 14 14:16:55 2021UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210414.cxs Log from Wed Apr 14 01:34:40 2021 Startup Messages --- note | Updating list of available bundles failed: Internal Server Error UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P9_J643_009_volume_map_filtered.mrc Opened cryosparc_P9_J643_009_volume_map_filtered.mrc, grid size 200,200,200, pixel 1.28, shown at level 0.402, step 1, values float32 > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp.mrc Opened cryosparc_P10_J41_005_volume_map_sharp.mrc, grid size 300,300,300, pixel 0.834, shown at level 0.231, step 2, values float32 > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_apo_210402_final.pdb Chain information for MRP4_apo_210402_final.pdb #3 --- Chain | Description A | No description available > open /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_ATP_bound.pdb Chain information for MRP4_ATP_bound.pdb #4 --- Chain | Description A | No description available > matchmaker #4 to #3 bring #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker MRP4_apo_210402_final.pdb, chain A (#3) with MRP4_ATP_bound.pdb, chain A (#4), sequence alignment score = 5507.9 RMSD between 494 pruned atom pairs is 1.064 angstroms; (across all 1125 pairs: 13.102) > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!2 models > show #!3 models > volume #1 level 0.854 > hide #!3 models > show #!3 models > hide #!1 models > select #3:start-80 530 atoms, 535 bonds, 1 model selected > hide #!3 models > show #!3 models > select #3:start-80 530 atoms, 535 bonds, 1 model selected > color sel red > color sel #FEE440 > select #3:80-390 5045 atoms, 5095 bonds, 1 model selected > view sel > view sel > set bgColor white > select #3:80-390 5045 atoms, 5095 bonds, 1 model selected > select #3:start-90 714 atoms, 722 bonds, 1 model selected > color sel #FEE440 > undo > select #3:start-89 692 atoms, 700 bonds, 1 model selected > color sel #FEE440 > select up 18454 atoms, 18642 bonds, 1 model selected > select up 27630 atoms, 28008 bonds, 6 models selected > select down 18454 atoms, 18642 bonds, 1 model selected > select down 692 atoms, 700 bonds, 1 model selected > select down 692 atoms, 700 bonds, 1 model selected > select down 692 atoms, 700 bonds, 1 model selected > select down 692 atoms, 700 bonds, 1 model selected > select #3:89-390 4888 atoms, 4937 bonds, 1 model selected > color sel #00bbf9 > select #3:89-391 4907 atoms, 4956 bonds, 1 model selected > color sel #00bbf9 > undo > undo > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > volume #1 level 0.9007 > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > select #3:391-615 3212 atoms, 3235 bonds, 4 pseudobonds, 2 models selected > color sel #00F5D4 > select #3:692-1018 5154 atoms, 5221 bonds, 2 pseudobonds, 2 models selected > color sel #9B5DE5 > select #3:1019-end 4532 atoms, 4572 bonds, 1 model selected > select up 18454 atoms, 18642 bonds, 1 model selected > select down 4532 atoms, 4572 bonds, 1 model selected > color sel #F15BB5 > select clear > show #!3 atoms > hide #!3 atoms > show #!1 models > volume #1 level 0.7916 > surface dust #1 size 5 update true > surface dust #1 size 10 update true > undo > show #!1 models > surface dust #1 size 15 update true > volume #1 level 0.9475 > volume #1 level 0.854 > surface dust #1 size 12 update true > surface dust #1 size 20 update true > surface dust #1 size 12 update true > undo > show #!1 models > surface dust #1 size 20 update true > color zone #1 near #3 distance 1 > color zone #1 near #3 distance 2 > color zone #1 near #3 distance 3 > color zone #1 near #3 distance 2 > hide #!3 models > show #!3 models > color zone #1 near #3 distance 4 > color zone #1 near #3 distance 3 > surface dust #1 size 25 update true > surface dust #1 size 20 update true > surface dust #1 size 25 update true > surface dust #1 size 30 update true > surface dust #1 size 25 update true > hide #!3 models > undo > undo > undo > undo > undo > undo > undo > undo > undo > select #3:89-390 4888 atoms, 4937 bonds, 1 model selected > select #3:89-391 4907 atoms, 4956 bonds, 1 model selected > select #3:1019-end 4532 atoms, 4572 bonds, 1 model selected > select #3:89-391 4907 atoms, 4956 bonds, 1 model selected > hide #!1 models > color sel #9B5DE5 > select #3:391-615 3212 atoms, 3235 bonds, 4 pseudobonds, 2 models selected > select #3:392-615 3193 atoms, 3216 bonds, 4 pseudobonds, 2 models selected > color sel #F15BB5 > select clear > select #3:692-1018 5154 atoms, 5221 bonds, 2 pseudobonds, 2 models selected > color sel #00BBF9 > select #3:1019-end 4532 atoms, 4572 bonds, 1 model selected > color sel #00F5D4 > show #!1 models > select clear > color zone #1 near #3 distance 3 > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > lighting full > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc Opened cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc, grid size 300,300,300, pixel 0.834, shown at level 0.205, step 2, values float32 > close #5 > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P9_J643_009_volume_map_filtered_gaussian.mrc Opened cryosparc_P9_J643_009_volume_map_filtered_gaussian.mrc, grid size 200,200,200, pixel 1.28, shown at level 0.386, step 1, values float32 > volume #5 level 0.1531 > volume #5 color #bcb1ff > volume #5 color #bfb3ff > volume #5 color #c1b5ff > volume #5 color #c4baff > volume #5 color #c7c2fe > volume #5 color #c7c5fe > volume #5 color #cccafe > volume #5 color #d1d0fd > volume #5 color #d3d2fd > volume #5 color #d4d5fd > volume #5 color #d8dafd > volume #5 color #d9dbfc > volume #5 color #d9dcfc > volume #5 color #dce0fc > volume #5 color #dee3fc > volume #5 color #e1e8fb > volume #5 color #e3ecfb > volume #5 color #e3eefb > volume #5 color #e4f0fb > volume #5 color #e4f1fb > volume #5 color #e4f2fb > volume #5 color #e3f3fb > volume #5 color #e1f5fb > volume #5 color #e0f4fb > volume #5 color #def2fb > volume #5 color #ddf1fb > volume #5 color #ddf0fb > volume #5 color #dceffb > volume #5 color #dbeefb > volume #5 color #dbedfb > volume #5 color #daecfb > volume #5 color #d8eafb > volume #5 color #d8e8fc > volume #5 color #d6e7fc > volume #5 color #d5e6fc > volume #5 color #d5e5fc > volume #5 color #d2e3fc > volume #5 color #d0e3fc > volume #5 color #cee2fc > volume #5 color #cde2fc > volume #5 color #cce1fc > volume #5 color #cbe1fc > volume #5 color #cae1fc > volume #5 color #c8e1fc > volume #5 color #c7e1fc > volume #5 color #c5e1fc > volume #5 color #c5e2fc > volume #5 color #c3e2fc > volume #5 color #c2e3fc > volume #5 color #c1e3fc > volume #5 color #c0e4fc > volume #5 color #c1e6fc > volume #5 color #c2e8fc > volume #5 color #c2e9fc > volume #5 color #c4eafc > volume #5 color #c6ebfc > volume #5 color #c8ebfc > volume #5 color #cdecfc > volume #5 color #d0edfb > volume #5 color #d1edfb > volume #5 color #d3edfb > volume #5 color #d4edfb > volume #5 color #d6eefb > volume #5 color #d8effb > volume #5 color #d9effb > volume #5 color #e0f1fb > volume #5 color #e1f1fb > volume #5 color #e0f1fb > volume #5 color #dcf1fb > volume #5 color #daf2fb > volume #5 color #d9f2fb > volume #5 color #d7f2fb > volume #5 color #d7f3fb > volume #5 color #dcf7fb > volume #5 color #dff9fa > volume #5 color #e0fafa > volume #5 color #e4fbfa > volume #5 color #e5fbf9 > volume #5 color #eafbf8 > volume #5 color #edfbf8 > volume #5 color #eefbf8 > volume #5 color #f0faf7 > volume #5 color #f0faf7fa > volume #5 color #f0faf7e9 > volume #5 color #f0faf7c0 > volume #5 color #f0faf780 > volume #5 color #f0faf737 > volume #5 color #f0faf711 > volume #5 color #f0faf700 > volume #5 color #f0faf709 > volume #5 color #f0faf711 > volume #5 color #f0faf713 > volume #5 color #f0faf719 > volume #5 color #f0faf71c > volume #5 color #f0faf71f > volume #5 color #f0faf722 > volume #5 color #f0faf723 > volume #5 color #f0faf726 > volume #5 color #f0faf727 > volume #5 color #f0faf723 > volume #5 color #f0faf722 > volume #5 color #f0faf721 > volume #5 color #f0faf720 > volume #5 color #f0faf71d > volume #5 color #f0faf71c > volume #5 color #f0faf71b > volume #5 color #f0faf71a > volume #5 color #f0faf718 > volume #5 color #f0faf715 > volume #5 color #f0faf713 > volume #5 color #f0faf711 > volume #5 color #f0faf708 > volume #5 color #f0faf707 > volume #5 color #f0faf706 > volume #5 color #f0faf705 > volume #5 color #f0faf704 > volume #5 color #f0faf702 > volume #5 color #f0faf700 > volume #5 color #f0faf709 > volume #5 color #f0faf70a > volume #5 color #f0faf70c > volume #5 color #f0faf70d > volume #5 color #f0faf70e > volume #5 color #f0faf70f > volume #5 color #f0faf70e > volume #5 color #f0faf70d > volume #5 color #f0faf70c > volume #5 color #f0faf70b > volume #5 color #f0faf70a > volume #5 color #f0faf70b > volume #5 color #f0faf70c > graphics silhouettes true > set silhouettes depthJump 1 Invalid ""silhouettes"" argument: Expected true or false (or 1 or 0) > set silhouettes true depthJump 1 Expected a keyword > graphics silhouettes true depthJump 1 > graphics silhouettes true depthJump 0.1 > graphics silhouettes true depthJump 0.01 > graphics silhouettes true depthJump 0.03 > graphics silhouettes true depthJump 0.5 > graphics silhouettes true depthJump 0.1 > graphics silhouettes true depthJump 1 > graphics silhouettes true depthJump .9 > graphics silhouettes true depthJump .8 > graphics silhouettes true depthJump .1 > graphics silhouettes true depthJump .2 > graphics silhouettes true depthJump .3 > graphics silhouettes true depthJump .4 > graphics silhouettes true depthJump .4 > graphics silhouettes true depthJump .3 > graphics silhouettes true width 1 depthJump .3 > graphics silhouettes true width .9 depthJump .3 > graphics silhouettes true width 2 depthJump .3 > volume #5 color #f1fbf80c > volume #5 color #f5fffc0c > volume #5 color #f0fff60c > volume #5 color #f0fff50c > volume #5 color #f0fff30c > volume #5 color #f0fff20c > volume #5 color #f0fff10c > volume #5 color #f1ffef0c > volume #5 color #f0ffee0c > volume #5 color #f1ffef0c > volume #5 color #f2fff00c > volume #5 color #f3fff20c > volume #5 color #f4fff30c > volume #5 color #f4fff40c > volume #5 color #f5fff40c > volume #5 color #f5fff50c > volume #5 color #f7fff60c > volume #5 color #f8fff60c > volume #5 color #f9fff60c > volume #5 color #fafff70c > volume #5 color #fafff80c > volume #5 color #f9fff90c > volume #5 color #f8fff90c > volume #5 color #f7fff90c > volume #5 color #f7fff90d > volume #5 color #f7fff90c > volume #5 color #f7fff90a > volume #5 color #f7fff904 > volume #5 color #f7fff900 > volume #5 color #f7fff909 > volume #5 color #f7fff90a > volume #5 color #f7fff90b > volume #5 color #f7fff90c > volume #5 color #f7fff90d > volume #5 color #f7fff90e > volume #5 color #f7fff90f > volume #5 color #f7fff910 > volume #5 color #f7fff911 > volume #5 color #f7fff912 > volume #5 color #f7fff913 > volume #5 color #f7fff914 > volume #5 color #f7fff915 > volume #5 color #f7fff916 > volume #5 color #f7fff917 > volume #5 color #f7fff918 > volume #5 color #f7fff919 > volume #5 color #f7fff91a > volume #5 color #f7fff91b > volume #5 color #f7fff91c > volume #5 color #f7fff91d > volume #5 color #f7fff91e > volume #5 color #f7fff91f > volume #5 color #f7fff920 > volume #5 color #f7fff921 > volume #5 color #f7fff923 > volume #5 color #f7fff924 > volume #5 color #f7fff926 > volume #5 color #f7fff927 > volume #5 color #f7fff929 > volume #5 color #f7fff92c > volume #5 color #f7fff92d > volume #5 color #f7fff92f > volume #5 color #f7fff930 > volume #5 color #f7fff931 > volume #5 color #f7fff932 > volume #5 color #f7fff933 > volume #5 color #f7fff935 > volume #5 color #f7fff934 > volume #5 color #f7fff92f > volume #5 color #f7fff928 > volume #5 color #f7fff922 > volume #5 color #f7fff91f > volume #5 color #f7fff91c > volume #5 color #f7fff918 > volume #5 color #f7fff916 > volume #5 color #f7fff918 > volume #5 color #f7fff91a > volume #5 color #f7fff91c > volume #5 color #f7fff91d > volume #5 color #f7fff920 > volume #5 color #f7fff922 > volume #5 color #f7fff924 > volume #5 color #f7fff925 > volume #5 color #f7fff924 > volume #5 color #f7fff923 > volume #5 color #f7fff922 > volume #5 color #f7fff921 > volume #5 color #f7fff91e > volume #5 color #f7fff91b > volume #5 color #f7fff918 > volume #5 color #f7fff916 > volume #5 color #f7fff915 > volume #5 color #f7fff914 > volume #5 color #f7fff913 > volume #5 color #f7fff912 > volume #5 color #f7fff911 > volume #5 color #f7fff90f > volume #5 color #f7fff90d > volume #5 color #f7fff90b > volume #5 color #f7fff908 > volume #5 color #f7fff907 > volume #5 color #f7fff906 > volume #5 color #f7fff905 > volume #5 color #f7fff902 > volume #5 color #f7fff900 > volume #5 color #f7fff909 > volume #5 color #f7fff90a > volume #5 color #f7fff90b Unknown data format: 'tiff' Unknown data format: '.tiff' Unknown data format: 'tif' > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff supersample 3 > transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff 2400 2400 > supersample 3 transparentBackground true Expected a keyword > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff width 2400 > height 2400 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a2.tiff width 800 > height 800 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a2.tiff width 2400 > height 2400 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2a.tiff width 2400 > height 2400 supersample 3 transparentBackground true > hide #!1 models > show #!3 models > hide #!5 models > lighting soft > lighting simple > lighting full > lighting full > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting flat > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > lighting simple > lighting soft > lighting flat > lighting soft > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2b.tiff width 2400 > height 2400 supersample 3 transparentBackground true > show #!5 models > hide #!5 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > view matrix camera position: -0.17269,0.019211,0.98479,521.56,-0.98139,-0.088602,-0.17037,56.059,0.083981,-0.99588,0.034155,148.7 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99244,0.031635,0.11859,-14.991,0.021502,-0.99608,0.085774,234.19,0.12084,-0.082575,-0.98923,249.89,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.99244,0.031635,0.11859,-14.991,0.021502,-0.99608,0.085774,234.19,0.12084,-0.082575,-0.98923,249.89,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0 > show #!2 models > hide #!3 models > hide #3.1 models > volume #2 step 1 > volume #2 level 0.5642 > show #!4 models > volume #2 level 0.436 > select #4:start-88 341 atoms, 347 bonds, 1 model selected > color sel #FEE440 > select #4:89-391 2396 atoms, 2445 bonds, 1 model selected > color sel #9B5DE5 > select #4:392-615 1665 atoms, 1690 bonds, 2 pseudobonds, 2 models selected > color sel #F15BB5 > select #4:692-1018 2422 atoms, 2488 bonds, 4 pseudobonds, 2 models selected > color sel #00BBF9 > select #4:1019-end 2352 atoms, 2393 bonds, 1 model selected > color sel #00F5D4 > select #4 9176 atoms, 9366 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > color zone #2 near #4 distance 3 > volume #1 color #b2b2b3 > color #2 #b2b2b3 > color zone #2 near #4 distance 3 > surface dust #2 size 25 update true > surface dust #2 size 30 update true > surface dust #2 size 40 update true > surface dust #2 size 50 update true > volume #2 level 0.6069 > surface dust #2 size 25 update true > volume #2 level 0.4531 > volume #2 level 0.5215 > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc Opened cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc, grid size 300,300,300, pixel 0.834, shown at level 0.205, step 2, values float32 > volume #6 step 1 > volume #6 level 0.2345 > save /Users/Hoodwinked/Data/For_Publication/Final_Models/figure_2.cxs > close > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc > /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_ATP_bound.pdb > /Users/Hoodwinked/Data/For_Publication/Final_Models/cryosparc_P10_J41_005_volume_map_sharp.mrc Chain information for MRP4_ATP_bound.pdb #2 --- Chain | Description A | No description available Opened cryosparc_P10_J41_005_volume_map_sharp_gaussian.mrc, grid size 300,300,300, pixel 0.834, shown at level 0.205, step 2, values float32 Opened cryosparc_P10_J41_005_volume_map_sharp.mrc, grid size 300,300,300, pixel 0.834, shown at level 0.231, step 2, values float32 > select #2:start-88 341 atoms, 347 bonds, 1 model selected > color sel #FEE440 > select #2:89-391 2396 atoms, 2445 bonds, 1 model selected > color sel #9B5DE5 > select #2:392-615 1665 atoms, 1690 bonds, 2 pseudobonds, 2 models selected > color sel #F15BB5 > select #2:692-1018 2422 atoms, 2488 bonds, 4 pseudobonds, 2 models selected > color sel #00BBF9 > select #2:1019-end 2352 atoms, 2393 bonds, 1 model selected > color sel #00F5D4 > select #2 9176 atoms, 9366 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > lighting soft > graphics silhouettes true width 2 depthJump .3 > volume #3 color #f7fff90b > show #!3 models > volume #3 step 1 > volume #3 level 0.2652 > undo > undo > hide sel atoms > volume #1 color #f7fff90b > volume #1 color #f7fff90a > volume #3 color #cdcdcd > volume #3 level 0.4873 > surface dust #3 size 25 update true > color zone #3 near #2 distance 3 > volume #3 level 0.5898 > surface dust #3 size 15 update true > surface dust #3 size 10 update true > surface dust #3 size 12 update true > surface dust #3 size 13 update true > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > volume #3 level 0.4617 > surface dust #3 size 15 update true > surface dust #3 size 20 update true > surface dust #3 size 25 update true > surface dust #3 size 20 update true > volume #1 level 0.08724 > volume #1 level 0.06653 > volume #1 step 1 > volume #1 level 0.06537 > volume #3 level 0.4617 > volume #3 level 0.5044 > surface dust #3 size 25 update true > surface dust #3 size 15 update true > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > lighting soft > lighting full > lighting full > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > volume #1 level 0.05143 > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > color zone #3 near #2 distance 4 > color zone #3 near #2 distance 5 > color zone #3 near #2 distance 6 > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > show #!2 models > hide #!1 models > hide #!3 models > select clear > hide #!2 models > show #!3 models > show #!1 models > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > hide #!1 models > hide #!3 models > show #!2 models > select ::name=""ATP"" 62 atoms, 66 bonds, 1 model selected > select ATP Expected an objects specifier or a keyword > select ::name=""ATP"",""Mg"" Expected an objects specifier or a keyword > select ::name=""ATP"" 62 atoms, 66 bonds, 1 model selected > select ::name=""ATP"" and sel ::name=""Mg"" Expected a keyword > select ::name=""ATP"" sel ::name=""Mg"" Expected a keyword > select ::name=""ATP,""""Mg"" Expected an objects specifier or a keyword > select ::name=""ATP"" 62 atoms, 66 bonds, 1 model selected > style sel sphere Changed 62 atom styles > show sel atoms > color sel byhetero > color sel grey > color sel byhetero > select clear > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2d.tiff width 2400 > height 2400 supersample 3 transparentBackground true > hide #!2 models > show #!1 models > show #!3 models > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2c.tiff width 2400 > height 2400 supersample 3 transparentBackground true > undo > show #!3 models > hide #!1 models > hide #!3 models > show #!2 models > select up Nothing selected > select ::name=""ATP"" 62 atoms, 66 bonds, 1 model selected > lighting grey Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword > select light grey Expected an objects specifier or a keyword > color light grey > undo > color sel light grey > color sel byhetero > select clear > select ::name=""ATP"" 62 atoms, 66 bonds, 1 model selected > color sel grey > color sel byhetero > select clear > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2d.tiff width 2400 > height 2400 supersample 3 transparentBackground true > select ::name=""ATP"" 62 atoms, 66 bonds, 1 model selected > color sel #FEE440 > color sel byhetero > select clear > save /Users/Hoodwinked/Data/For_Publication/Figure_2/A/2d_v2.tiff width 2400 > height 2400 supersample 3 transparentBackground true > select #2:757 9 atoms, 8 bonds, 1 model selected > volume #3 level 0.3848 > volume #3 level 0.4531 > open /Users/Hoodwinked/Desktop/cynthia/2o1v_lpf.mrc Opened 2o1v_lpf.mrc, grid size 256,256,256, pixel 1.44, shown at level 130, step 1, values float32 > volume #4 level 310.1 > close #4 > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > close #3 > close #1 > open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/aligned_MRP4_apo.pdb Chain information for aligned_MRP4_apo.pdb #1 --- Chain | Description A | No description available > close #1 > close > open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/aligned_MRP4_apo.pdb Chain information for aligned_MRP4_apo.pdb #1 --- Chain | Description A | No description available > open /Users/Hoodwinked/Data/For_Publication/Figure_4/A/MRP4_ATP_bound.pdb Chain information for MRP4_ATP_bound.pdb #2 --- Chain | Description A | No description available > hide #!1 models > show #!1 models > hide atoms > hide atoms > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting flat > lighting soft > lighting full > lighting soft > modeHelix tube Unknown command: modeHelix tube > modehelix Unknown command: modehelix > cartoon style protein cylinders Expected a keyword > cartoon style protein cylinders Expected a keyword > cartoon style protein cylinder Expected a keyword > cartoon style protein modeHelix tube > cartoon style protein modeHelix cylinder Invalid ""modeHelix"" argument: Should be one of 'default', 'tube', or 'wrap' > cartoon style protein modeHelix cylinders Invalid ""modeHelix"" argument: Should be one of 'default', 'tube', or 'wrap' > cartoon style protein modeHelix wrap > cartoon style protein modeHelix default > cartoon style protein modeHelix wrap > cartoon style protein modeHelix tube > cartoon style protein modeHelix default > open > /Users/Hoodwinked/Data/For_Publication/Final_Models/MRP4_apo_210402_final.pdb Chain information for MRP4_apo_210402_final.pdb #3 --- Chain | Description A | No description available > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker aligned_MRP4_apo.pdb, chain A (#1) with MRP4_apo_210402_final.pdb, chain A (#3), sequence alignment score = 5847.8 RMSD between 1139 pruned atom pairs is 0.156 angstroms; (across all 1144 pairs: 0.719) > hide #!2 models > hide #!3 models > show #!3 models > close #1 > show #!2 models Cannot determine format for '#3' Cannot determine format for '#3' > save #3 /Data/For_Publication/Figure_4/A/apo_aligned_use.pdb format pdb Expected a models specifier or a keyword > save /Data/For_Publication/Figure_4/A/apo_aligned_use.pdb pdb #3 Expected a models specifier or a keyword > save /Data/For_Publication/Figure_4/A/apo_aligned_use.pdb format pdb models > #3 Traceback (most recent call last): File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/save_command/cmd.py"", line 79, in provider_save mgr).save(session, path, **provider_kw) File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/__init__.py"", line 70, in save pdb.save_pdb(session, path, **kw) File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 119, in save_pdb (serial_numbering == ""h36""), polymeric_res_names) OSError: Unable to open file '/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb' for writing OSError: Unable to open file '/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb' for writing File ""/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 119, in save_pdb (serial_numbering == ""h36""), polymeric_res_names) See log for complete Python traceback. > save /Users/Hoodwinked/Data/For_Publication/Figure_4/Aapo_aligned_use.pdb > format pdb models #3 > save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb > format pdb models #3 > save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/apo_aligned_use.pdb > format pdb models #3 > select #:391 Expected an objects specifier or a keyword > select :391 27 atoms, 25 bonds, 2 models selected > select :390-696 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > hide sel cartoons > select :1018-end 6904 atoms, 6985 bonds, 2 models selected > hide sel cartoons > select up 6939 atoms, 7021 bonds, 2 models selected > select up 27630 atoms, 28008 bonds, 2 models selected > select up 27630 atoms, 28008 bonds, 2 models selected > select down 6939 atoms, 7021 bonds, 2 models selected > select down 6904 atoms, 6985 bonds, 2 models selected > select down 6904 atoms, 6985 bonds, 2 models selected > select down 6904 atoms, 6985 bonds, 2 models selected > view sel > ui tool show ""Side View"" > cartoon style protein modeHelix tube > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > cartoon style protein modeHelix default > select #:697-860 Expected an objects specifier or a keyword > select :697-860 3768 atoms, 3836 bonds, 4 pseudobonds, 4 models selected > color sel grey > color sel light grey > color sel stone Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel grey > select :974-1017 1028 atoms, 1036 bonds, 2 models selected > color sel grey > select up 1105 atoms, 1113 bonds, 2 models selected > select up 27630 atoms, 28008 bonds, 2 models selected > select :233-345 2745 atoms, 2771 bonds, 2 models selected > color sel grey > select #3/A:1017 14 atoms, 13 bonds, 1 model selected > select clear > select grey and #1 Expected an objects specifier or a keyword > select grey and #2 Expected an objects specifier or a keyword > hide cartoons > hide cartoons > show cartoons > show cartoons > select :390-696 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > hide sel cartoons > select up 5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected > select down 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > select :1018-end 6904 atoms, 6985 bonds, 2 models selected > hide sel cartoons > select :233-345 2745 atoms, 2771 bonds, 2 models selected > transperancy sel 50 Unknown command: transperancy sel 50 > transparancy sel 50 Unknown command: transparancy sel 50 > select transparency 50 Expected an objects specifier or a keyword > transparency 50 > transparency 50 target r > transparency 0 target r > transparency 0 sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select transparency 0 Expected an objects specifier or a keyword > transparency 0 > transparency 50 > transparency 50 target sel Invalid ""target"" argument: Character 'e' is not an allowed target, must be one of acrsbpfl > transparency sel 50 target cartoon Invalid ""target"" argument: Character 't' is not an allowed target, must be one of acrsbpfl > transparency sel 50 cartoons > select clear > select :390-696 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > hide sel cartoons > show sel cartoons > hide sel cartoons > select up 5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected > select up 27630 atoms, 28008 bonds, 10 pseudobonds, 4 models selected > select down 5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected > select down 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > select up 5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected > select up 27630 atoms, 28008 bonds, 10 pseudobonds, 4 models selected > select down 5580 atoms, 5635 bonds, 10 pseudobonds, 4 models selected > select down 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > select down 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > transparency 50 > select :390-696 4990 atoms, 5036 bonds, 10 pseudobonds, 4 models selected > select :233-345 2745 atoms, 2771 bonds, 2 models selected > transparency sel 100 cartoons > transparency sel 0 cartoons > select :233-345 2745 atoms, 2771 bonds, 2 models selected > select :233-345 2745 atoms, 2771 bonds, 2 models selected > select :974-1017 1028 atoms, 1036 bonds, 2 models selected > select :697-860 3768 atoms, 3836 bonds, 4 pseudobonds, 4 models selected > select :233-345,697-860,974-1017 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > transparency sel 50 cartoons > select clear > transparency sel 25 cartoons > select :233-345,697-860,974-1017 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > transparency sel 25 cartoons > select clear > transparency sel 75 cartoons > select :233-345,697-860,974-1017 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > transparency sel 25 cartoons > transparency sel 80 cartoons > transparency sel 75 cartoons > select clear > select :48-232 4445 atoms, 4515 bonds, 2 models selected > hide sel atoms > hide sel cartoons > show sel cartoons > show sel cartoons > show sel cartoons > select :346-398 1218 atoms, 1230 bonds, 2 models selected > select :861-973 2682 atoms, 2735 bonds, 2 pseudobonds, 3 models selected > select #2:233-345,974-1017,861-973 2042 atoms, 2086 bonds, 2 pseudobonds, 2 models selected > select #2:233-345,974-1017 1236 atoms, 1253 bonds, 1 model selected > select #2:233-345,974-1017,697-860 2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected > transparency sel 0 cartoons > color sel grey > color sel light grey > select clear > select :233-345,974-1017,697-860 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > transparency sel 0 cartoons > select clear > ui mousemode right select Drag select of 6 pseudobonds, 1293 residues > cartoon style protein modeHelix tube > cartoon style protein modeHelix licorice Invalid ""modeHelix"" argument: Should be one of 'default', 'tube', or 'wrap' > cartoon style protein modeHelix default > cartoon style protein modeHelix tube > select clear > select clear > undo > cartoon style protein modeHelix default > select :47-390,617-1018 15861 atoms, 16106 bonds, 6 pseudobonds, 4 models selected > select :47-390 8285 atoms, 8397 bonds, 2 models selected > select clear > select :47-232 4452 atoms, 4522 bonds, 2 models selected > select clear > select :346-389 1061 atoms, 1073 bonds, 2 models selected > select :47-232,346-389,861-973 8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected > select :47-232 4452 atoms, 4522 bonds, 2 models selected > select :47-79 780 atoms, 790 bonds, 2 models selected > color sel #FEE440 > sel:80-232,346-389,861-973 Unknown command: sel:80-232,346-389,861-973 > select :80-232,346-389,861-973 7415 atoms, 7538 bonds, 2 pseudobonds, 3 models selected > color sel #9B5DE5 > select :46-232,346-389,861-973 8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 50 cartoons > transparency sel 90 cartoons > select clear > transparency sel 75 cartoons > transparency sel 65 cartoons > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 65 cartoons > select clear > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 70 cartoons > select clear > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select :47-232,346-389,861-973 8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select :47-232,346-389,861-973 8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected > select :47-232,346-389,861-973 8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected > select :47-232,346-389,861-973 8195 atoms, 8330 bonds, 2 pseudobonds, 3 models selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select #2:233-345,974-1017,697-860 2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected > select #:233-345,974-1017,697-860 Expected an objects specifier or a keyword > select :233-345,974-1017,697-860 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > color sel grey > select clear > select :233-345,974-1017,697-860 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > select :233-345,974-1017,697-860 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > color sel #e3dac9 > select clear > select clear > select :233-345,974-1017,697-860 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > select #2:233-345,974-1017,697-860 2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected > select clear > transparency sel 70 cartoons > select #2:233-345,974-1017,697-860 2494 atoms, 2545 bonds, 2 pseudobonds, 2 models selected > select :233-345,974-1017,697-860 7541 atoms, 7643 bonds, 4 pseudobonds, 4 models selected > select #2:46-232,346-389,861-973 2634 atoms, 2701 bonds, 2 pseudobonds, 2 models selected > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 80 cartoons > select clear > select clear > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting flat > lighting soft > select :1018-end 6904 atoms, 6985 bonds, 2 models selected > show sel cartoons > color sel bone Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel #e3dac9 > select clear > select :389-600 4586 atoms, 4636 bonds, 6 pseudobonds, 4 models selected > show sel cartoons > select :390-600 4555 atoms, 4603 bonds, 6 pseudobonds, 4 models selected > color sel #F15BB5 > select #3:390-600 2989 atoms, 3012 bonds, 4 pseudobonds, 2 models selected > transparency sel 80 cartoons > select clear > save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210414.cxs > select up Nothing selected > select :1018-end 6904 atoms, 6985 bonds, 2 models selected > hide sel cartoons > select :391-600 4528 atoms, 4576 bonds, 6 pseudobonds, 4 models selected > hide sel cartoons > select #2/A:390 8 atoms, 7 bonds, 1 model selected > hide sel atoms > hide sel cartoons > save /Users/Hoodwinked/Desktop/image22.png supersample 3 > save /Users/Hoodwinked/Desktop/image22.png supersample 3 > transparentBackground true > save /Users/Hoodwinked/Desktop/image22.png supersample 3 > transparentBackground true > save /Users/Hoodwinked/Desktop/image22.png supersample 3 > transparentBackground true > save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210414.cxs opened ChimeraX session > select up 625 atoms, 632 bonds, 2 models selected > select clear > save /Users/Hoodwinked/Desktop/image22.tiff supersample 3 > transparentBackground true > save /Users/Hoodwinked/Desktop/image22.tiff 2400 2400 supersample 3 > transparentBackground true Expected a keyword > save /Users/Hoodwinked/Desktop/image22.tiff 2400 supersample 3 > transparentBackground true Expected a keyword > save /Users/Hoodwinked/Desktop/image22.tiff supersample 3 2400 2400 > transparentBackground true Expected a keyword > save /Users/Hoodwinked/Desktop/image22.tiff supersample 3 width 2400 height > 2400 transparentBackground true > save /Users/Hoodwinked/Desktop/image222.tiff supersample 3 width 2400 height > 2400 transparentBackground true > select #3:390-600 2989 atoms, 3012 bonds, 4 pseudobonds, 2 models selected > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 60 cartoons > select clear > select clear > save /Users/Hoodwinked/Desktop/image22260.tiff supersample 3 width 2400 > height 2400 transparentBackground true > transparency sel 70 cartoons > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 70 cartoons > save /Users/Hoodwinked/Desktop/image22270.tiff supersample 3 width 2400 > height 2400 transparentBackground true > select clear > select #3:46-232,346-389,861-973 5561 atoms, 5629 bonds, 1 model selected > transparency sel 80 cartoons > save /Users/Hoodwinked/Desktop/image22280.tiff supersample 3 width 2400 > height 2400 transparentBackground true > select clear > save /Users/Hoodwinked/Desktop/image22280.tiff supersample 3 width 2400 > height 2400 transparentBackground true > angle #2.281;342;916 short Unknown command: angle #2.281;342;916 short > angle #2.281 #2.342 #2.916 short Unknown command: angle #2.281 #2.342 #2.916 short > angle #2:281 #2:342 #2:916 short Unknown command: angle #2:281 #2:342 #2:916 short > save /Users/Hoodwinked/Data/For_Publication/Figure_4/A/20210415.cxs opened ChimeraX session > angle #2:281 #2:342 #2:916 short angle is provided by the uninstalled bundle SEQCROW Downloading bundle SEQCROW-0.25.2-py3-none-any.whl Traceback (most recent call last): File ""/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/help_viewer/tool.py"", line 389, in download_finished session=self.session) File ""/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 903, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolshed_utils/__init__.py"", line 213, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle.name) AttributeError: 'str' object has no attribute 'name' AttributeError: 'str' object has no attribute 'name' File ""/programs/i386-mac/chimerax/1.1.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolshed_utils/__init__.py"", line 213, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle.name) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 1037.100.359.0.0 (iBridge: 17.16.14263.0.0,0) Software: System Software Overview: System Version: macOS 10.15.4 (19E266) Kernel Version: Darwin 19.4.0 Time since boot: 49 days 3 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.01.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal LED Cinema Display: Display Type: LCD Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 2A0292VN0K0 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: Thunderbolt/DisplayPort PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 biopython: 1.78 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StrudelScore: 0.1.3 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 mrcfile: 1.3.0 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 pandas: 1.2.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 recordtype: 1.3 requests: 2.24.0 scipy: 1.4.1 Send2Trash: 1.5.0 SEQCROW: 0.25.2 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 threed-strudel: 0.6 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal 1.3 Tool Shed fixed Eric Pettersen all ChimeraX