id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17354 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.2.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/MARV_model_Jan2025/marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb Chain information for marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb #1 --- Chain | Description A H | No description available B F | No description available C G K | No description available D I | No description available E | No description available J | No description available L | No description available > open > /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/MARV_model_Jan2025/MARV_MR72_DeepEM_J987flipped.mrc Opened MARV_MR72_DeepEM_J987flipped.mrc as #2, grid size 370,370,370, pixel 0.66, shown at level 0.00201, step 2, values float32 > volume #2 step 1 > volume #2 level 0.06089 > show cartoons > style stick Changed 11598 atom styles > open > /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/2024October_model/EBOV_MR72_refinement21-coot-0_glyco.pdb Chain information for EBOV_MR72_refinement21-coot-0_glyco.pdb #3 --- Chain | Description A B C | No description available D E F | No description available G I K | No description available H L | No description available J | No description available > open > /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/2024October_model/J638_EBOV_Mr72_DeepEM.mrc Opened J638_EBOV_Mr72_DeepEM.mrc as #4, grid size 370,370,370, pixel 0.66, shown at level 0.00161, step 2, values float32 > volume #4 step 1 > volume #4 level 0.05678 > mmaker #3 to #1 bring #4 Computing secondary structure 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 marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb, chain B (#1) with EBOV_MR72_refinement21-coot-0_glyco.pdb, chain H (#3), sequence alignment score = 602.8 RMSD between 119 pruned atom pairs is 0.470 angstroms; (across all 120 pairs: 1.128) > style stick Changed 23091 atom styles > show cartoons > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > hide #!3 models > hide #!4 models > hide #!2 models > select add #1 11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 1/E Alignment identifier is 1/J Alignment identifier is 1/L Alignment identifier is 4 > select subtract #1 Nothing selected > select #1/K,C,G:40 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/K,C,G:40-41 45 atoms, 42 bonds, 6 residues, 1 model selected > select #1/K,C,G:35 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/K,C,G:35-180 3411 atoms, 3498 bonds, 438 residues, 1 model selected > select #1/D,I:471 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/D,I:471-600 1576 atoms, 1608 bonds, 6 pseudobonds, 196 residues, 2 models selected > select #1/L:471-472 13 atoms, 13 bonds, 2 residues, 1 model selected > select #1/L:471-614 872 atoms, 889 bonds, 3 pseudobonds, 112 residues, 2 models selected > select #1/B,F:1 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/B,F:1-64 902 atoms, 928 bonds, 2 pseudobonds, 116 residues, 2 models selected > select #1/J:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/J:2-58 390 atoms, 400 bonds, 1 pseudobond, 51 residues, 2 models selected > select #1/D,I:471-472 26 atoms, 26 bonds, 4 residues, 1 model selected > select #1/D,I:471-554 820 atoms, 840 bonds, 6 pseudobonds, 104 residues, 2 models selected > select #1/L:474 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/L:474-608 812 atoms, 827 bonds, 3 pseudobonds, 103 residues, 2 models selected > select #1/J:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/J:2-58 390 atoms, 400 bonds, 1 pseudobond, 51 residues, 2 models selected > select #1/E:3 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/E:3-108 784 atoms, 804 bonds, 106 residues, 1 model selected > select #1/B,F:1 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/B,F:1-24 258 atoms, 256 bonds, 2 pseudobonds, 36 residues, 2 models selected > select #1/A,H:2 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/A,H:2-19 246 atoms, 250 bonds, 36 residues, 1 model selected > color #1/C/G/K #30924D > select add #1 11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected > select subtract #1 Nothing selected > color #1/D/I/L #667255 > color #1/B/F/J #FFB300 > color #1/E/A/H #CC9D1C > color :NAG,BMA,MAN peach puff > lighting soft > show #!2 models > cartoon style thickness 1.2 > hide #!2 models > show #!2 models > volume #2 level 0.08514 Unsupported scale factor (0.000000) detected on Display2 > view orient > color zone #2 near #1 distance 3.96 > volume splitbyzone #2 Opened MARV_MR72_DeepEM_J987flipped.mrc 0 as #5.1, grid size 370,370,370, pixel 0.66, shown at level 0.0851, step 1, values float32 Opened MARV_MR72_DeepEM_J987flipped.mrc 1 as #5.2, grid size 370,370,370, pixel 0.66, shown at level 0.0851, step 1, values float32 Opened MARV_MR72_DeepEM_J987flipped.mrc 2 as #5.3, grid size 370,370,370, pixel 0.66, shown at level 0.0851, step 1, values float32 Opened MARV_MR72_DeepEM_J987flipped.mrc 3 as #5.4, grid size 370,370,370, pixel 0.66, shown at level 0.0851, step 1, values float32 Opened MARV_MR72_DeepEM_J987flipped.mrc 4 as #5.5, grid size 370,370,370, pixel 0.66, shown at level 0.0851, step 1, values float32 Opened MARV_MR72_DeepEM_J987flipped.mrc 5 as #5.6, grid size 370,370,370, pixel 0.66, shown at level 0.0851, step 1, values float32 > hide #!5.1 models > surface dust Missing or invalid ""surfaces"" argument: empty atom specifier > surface dust #5 > volume #5.2 level 0.1421 > volume #5.3 level 0.142 > volume #5.4 level 0.142 > volume #5.5 level 0.142 > volume #5.6 level 0.142 > hide #!1 models > ui tool show ""Side View"" > show #!4 models > show #!3 models > hide #!5 models > hide #!4 models > select add #3 11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3/J Alignment identifier is 3 Alignment identifier is 4 > select subtract #3 Nothing selected > select #3/C,B,A:32 18 atoms, 15 bonds, 3 residues, 1 model selected > select #3/C,B,A:32-79 1053 atoms, 1056 bonds, 144 residues, 1 model selected > select #3/C,B,A:32 18 atoms, 15 bonds, 3 residues, 1 model selected > select #3/C,B,A 3583 atoms, 3676 bonds, 471 residues, 1 model selected > select #3/H,L:1-5 86 atoms, 84 bonds, 10 residues, 1 model selected > select #3/H,L:1-52 794 atoms, 814 bonds, 104 residues, 1 model selected > select #3/F,E,D:505 21 atoms, 18 bonds, 3 residues, 1 model selected > select #3/F,E,D:505-607 2303 atoms, 2363 bonds, 3 pseudobonds, 291 residues, 2 models selected > select #3/J:2-5 34 atoms, 33 bonds, 4 residues, 1 model selected > select #3/J:4-17 100 atoms, 101 bonds, 14 residues, 1 model selected > select #3/J:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/J:2-126 964 atoms, 993 bonds, 125 residues, 1 model selected > select #3/H,L:1-49 758 atoms, 778 bonds, 98 residues, 1 model selected > select #3/H,L:1-53 810 atoms, 830 bonds, 106 residues, 1 model selected > select #3/G,K,I:2-3 39 atoms, 36 bonds, 6 residues, 1 model selected > select #3/G,K,I:2-49 1047 atoms, 1074 bonds, 144 residues, 1 model selected > select add #3 11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected > select subtract #3 Nothing selected > color #3/A/B/C #00468D > color #3/D/E/F #335C71 > color #3/J/H/L #FFB300 > color #3/G/I/K #CC9D1C > color :NAG,BMA,MAN peach puff > toolshed show > show #!4 models > color zone #4 near #3 distance 3.96 > volume #4 level 0.09687 > ui tool show ""Side View"" > volume splitbyzone #4 Opened J638_EBOV_Mr72_DeepEM.mrc 0 as #6.1, grid size 370,370,370, pixel 0.66, shown at level 0.0969, step 1, values float32 Opened J638_EBOV_Mr72_DeepEM.mrc 1 as #6.2, grid size 370,370,370, pixel 0.66, shown at level 0.0969, step 1, values float32 Opened J638_EBOV_Mr72_DeepEM.mrc 2 as #6.3, grid size 370,370,370, pixel 0.66, shown at level 0.0969, step 1, values float32 Opened J638_EBOV_Mr72_DeepEM.mrc 3 as #6.4, grid size 370,370,370, pixel 0.66, shown at level 0.0969, step 1, values float32 Opened J638_EBOV_Mr72_DeepEM.mrc 4 as #6.5, grid size 370,370,370, pixel 0.66, shown at level 0.0969, step 1, values float32 Opened J638_EBOV_Mr72_DeepEM.mrc 5 as #6.6, grid size 370,370,370, pixel 0.66, shown at level 0.0969, step 1, values float32 > hide #!6.1 models > surface dust #6 > hide #!6 models > show #!6 models > hide #!3 models > show #!5 models > hide #!5 models > show #!5 models > mmaker #1/B to #3/B bring #5 Computing secondary structure 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 EBOV_MR72_refinement21-coot-0_glyco.pdb, chain B (#3) with marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb, chain B (#1), sequence alignment score = 22.1 RMSD between 5 pruned atom pairs is 1.503 angstroms; (across all 37 pairs: 20.017) > show #!3 models > show #!1 models > hide #!5 models > hide #!6 models > mmaker #1/C to #3/B bring #5 Computing secondary structure 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 EBOV_MR72_refinement21-coot-0_glyco.pdb, chain B (#3) with marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb, chain C (#1), sequence alignment score = 382.6 RMSD between 124 pruned atom pairs is 0.670 angstroms; (across all 138 pairs: 1.330) > hide #!3 models > show #!2 models > hide #!2 models > show #!5 models > hide #!1 models > show #!6 models > hide #!5 models > show #!5 models > hide #!6 models > show #!4 models > hide #!5 models > hide #!4 models > show #!6 models > show #!5 models > hide #!6 models > save /Users/tgewering/Desktop/MARV_GP_MR72_density.tif width 1344 height 903 > supersample 4 transparentBackground true > show #!6 models > hide #!5 models > save /Users/tgewering/Desktop/EBOV_GP_MR72_density.tif width 1344 height 903 > supersample 4 transparentBackground true > show #!3 models > hide #!6 models > lighting soft > hide atoms > set bgColor white > graphics silhouettes true width 5 > camera ortho > cartoon suppressBackboneDisplay false > lighting model #1,2 depthCue false > cartoon style protein modeHelix default arrows false xsection oval width 2 > thickness 2 > show cartoons > style stick Changed 23091 atom styles > graphics silhouettes true width 3 > show :NAG,BMA,MAN > size stickRadius 0.4 Changed 23716 bond radii > color byhetero > show #3/D/E/F:563 > show #3/D:563 > show #3/E:563 > show #3/F:563 > hide #!3 models > show #!3 models > show #3/J:30 > show #3/H:30 > show #3/L:30 > show atoms > hide atoms > show :NAG > show :563 > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > lighting model #1,2 depthCue true > show #!3 models > hide #!3 models > save /Users/tgewering/Desktop/MARV_GP_MR72_modeltif.tif width 1344 height > 903 supersample 4 transparentBackground true > show #!3 models > hide #!1 models > save /Users/tgewering/Desktop/EBOV_GP_MR72_model.tif width 1344 height 903 > supersample 4 transparentBackground true > show #!1 models > show #!2 models > hide #!3 models > hide #!2 models > show #!5 models > hide #!1 models > save /Users/tgewering/Desktop/MARV_GP_MR72_density.tif width 1344 height 903 > supersample 4 transparentBackground true > show #!6 models > hide #!5 models > save /Users/tgewering/Desktop/EBOV_GP_MR72_density.tif width 1344 height 903 > supersample 4 transparentBackground true > hide #!6 models > show #!1 models > turn x 90 > save /Users/tgewering/Desktop/MARV_GP_MR72_model_top.tif width 1344 height > 903 supersample 4 transparentBackground true > show #!3 models > hide #!1 models > save /Users/tgewering/Desktop/EBOV_GP_MR72_model_top.tif width 1344 height > 903 supersample 4 transparentBackground true > show #!1 models > hide #!3 models > turn x -90 > show #!6 models > show #!5 models > show #!4 models > hide #!4 models > show #!3 models > view orient > hide #!5 models > hide #!6 models > hide #!3 models > show #!3 models > hide /J/H/L > hide /J/H/L ribbons > hide /G/I/K ribbons > undo > hide #3:/G/I/K ribbons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #3/G/I/K ribbons > hide #1/B/F/J ribbons > hide #1/E/A/H ribbons > ui mousemode right zoom > ui tool show ""Similar Structures"" > select add #1 11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 1/E Alignment identifier is 1/J Alignment identifier is 1/L Alignment identifier is 4 > select #1/D,I:471 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/D,I:471-604 1634 atoms, 1666 bonds, 6 pseudobonds, 204 residues, 2 models selected > select #1/D,I:471 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/D,I:471-614 1770 atoms, 1806 bonds, 6 pseudobonds, 224 residues, 2 models selected > select #1/K,C,G:35-36 39 atoms, 36 bonds, 6 residues, 1 model selected > select #1/K,C,G:35-38 75 atoms, 72 bonds, 12 residues, 1 model selected > select #1/B,F:2 16 atoms, 14 bonds, 2 residues, 1 model selected > select #1/B,F:2-23 226 atoms, 224 bonds, 2 pseudobonds, 32 residues, 2 models selected > select #1/A,H:2 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/A,H:2-21 274 atoms, 278 bonds, 40 residues, 1 model selected > select #1/K,C,G:35 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/K,C,G:35-42 159 atoms, 156 bonds, 24 residues, 1 model selected > select #1/B,F:1 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/B,F:1-80 1152 atoms, 1180 bonds, 2 pseudobonds, 148 residues, 2 models selected > select #1/L:471 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/L:471-614 872 atoms, 889 bonds, 3 pseudobonds, 112 residues, 2 models selected > select #1/D,I:473 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/D,I:473-556 824 atoms, 842 bonds, 6 pseudobonds, 104 residues, 2 models selected > select #1/D,I:471 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1/D,I:471-614 1770 atoms, 1806 bonds, 6 pseudobonds, 224 residues, 2 models selected > select #1/C 1190 atoms, 1223 bonds, 150 residues, 1 model selected Alignment identifier is 1/C > select #1/C:35 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/C:35-180 1137 atoms, 1166 bonds, 146 residues, 1 model selected > select #2/C Nothing selected > select add #3 11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected > hide #!1 models > select #23/C Nothing selected > select #3/C 1195 atoms, 1226 bonds, 157 residues, 1 model selected Alignment identifier is 3/C > select #3/C:32 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/C 1195 atoms, 1226 bonds, 157 residues, 1 model selected > select #3/D 852 atoms, 876 bonds, 1 pseudobond, 106 residues, 2 models selected Alignment identifier is 3/D > select #3/D:504 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/D:504-612 813 atoms, 834 bonds, 1 pseudobond, 103 residues, 2 models selected > select add #3 11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected > select subtract #3 Nothing selected > open /Users/tgewering/Downloads/MARV_EBOV_aligned.praln Unrecognized file suffix '.praln' > open /Users/tgewering/Downloads/MARV_EBOV_aligned.praln Unrecognized file suffix '.praln' > open /Users/tgewering/Downloads/MARV_EBOV_aligned.aln Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 132, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 215, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 526, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 497, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/__init__.py"", line 74, in open return open_file(session, data, file_name, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/parse.py"", line 44, in open_file seqs, file_attrs, file_markups = ns['read'](session, stream) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/io/readALN.py"", line 36, in read for line in f.readlines(): ^^^^^^^^^^^^^ File """", line 322, in decode UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 23: invalid start byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 23: invalid start byte File """", line 322, in decode See log for complete Python traceback. > open /Users/tgewering/Downloads/MARV_EBOV_aligned.aln Failed opening file /Users/tgewering/Downloads/MARV_EBOV_aligned.aln: 'utf-8' codec can't decode byte 0xfc in position 23: invalid start byte > open /Users/tgewering/Downloads/MARV_EBOV_aligned.fa Summary of feedback from opening /Users/tgewering/Downloads/MARV_EBOV_aligned.fa --- notes | Alignment identifier is MARV_EBOV_aligned.fa Showing conservation header (""seq_conservation"" residue attribute) for alignment MARV_EBOV_aligned.fa Opened 2 sequences from MARV_EBOV_aligned.fa > select clear > hide #!3 models > show #!3 models > select clear > show #!1 models > hide #!3 models > select clear > color byattribute seq_conservation palette blue:red:yellow 23091 atoms, 2984 residues, atom seq_conservation range 100 to 100 > color byattribute seq_conversation No known/registered numeric attribute seq_conversation > color byattribute seq_conservation 23091 atoms, 2984 residues, atom seq_conservation range 100 to 100 > open /Users/tgewering/Downloads/MARV_EBOV_aligned.fa Summary of feedback from opening /Users/tgewering/Downloads/MARV_EBOV_aligned.fa --- notes | Alignment identifier is MARV_EBOV_aligned.fa Showing conservation header (""seq_conservation"" residue attribute) for alignment MARV_EBOV_aligned.fa Opened 2 sequences from MARV_EBOV_aligned.fa > color byattribute seq_conservation 23091 atoms, 2984 residues, atom seq_conservation range 100 to 100 > color byattribute seq_conservation 23091 atoms, 2984 residues, atom seq_conservation range 100 to 100 > color byattribute seq_conservation 23091 atoms, 2984 residues, atom seq_conservation range 100 to 100 > color byattribute seq_conservation 23091 atoms, 2984 residues, atom seq_conservation range 100 to 100 > select add #1 11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 1/E Alignment identifier is 1/J Alignment identifier is 1/L Alignment identifier is 4 > select #1/J:5 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/J:5-60 384 atoms, 395 bonds, 1 pseudobond, 50 residues, 2 models selected > select #1/K,C,G:35-36 39 atoms, 36 bonds, 6 residues, 1 model selected > select #1/K,C,G:35-41 132 atoms, 129 bonds, 21 residues, 1 model selected > select #1/K,C,G:41 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/K,C,G:41-180 3303 atoms, 3390 bonds, 420 residues, 1 model selected > select #1/K,C,G:35 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/K,C,G:35-180 3411 atoms, 3498 bonds, 438 residues, 1 model selected > select add #3 14904 atoms, 15304 bonds, 3 pseudobonds, 1934 residues, 3 models selected > select add #1 23091 atoms, 23716 bonds, 16 pseudobonds, 2984 residues, 4 models selected > select subtract #1 11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected > show #!3 models > hide #!1 models > select #3/A 1199 atoms, 1230 bonds, 157 residues, 1 model selected Alignment identifier is 3/A > select #3/A:32 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A 1199 atoms, 1230 bonds, 157 residues, 1 model selected > open /Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa Summary of feedback from opening /Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa --- notes | Alignment identifier is EBOV_MARV_GP1_aligned.fa Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to MARV_GP1 (0 aa) with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to MARV_GP1 (0 aa) with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to MARV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 (0 aa) with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment EBOV_MARV_GP1_aligned.fa Opened 2 sequences from EBOV_MARV_GP1_aligned.fa > select #1/C,G,K:36-38 57 atoms, 54 bonds, 9 residues, 1 model selected > select #1/C,G,K:36-49 315 atoms, 315 bonds, 42 residues, 1 model selected > select add #1 11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected > select subtract #1 Nothing selected > show #!1 models > select #1/C,G,K:36 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/C,G,K:36-111 1725 atoms, 1761 bonds, 228 residues, 1 model selected > undo > select subtract #3 Nothing selected > select add #3 11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected > select subtract #3 Nothing selected > show #!1 models > open /Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa Summary of feedback from opening /Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa --- notes | Alignment identifier is EBOV_MARV_GP1_aligned.fa Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to MARV_GP1 (0 aa) with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to MARV_GP1 (0 aa) with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to MARV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 (0 aa) with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment EBOV_MARV_GP1_aligned.fa Opened 2 sequences from EBOV_MARV_GP1_aligned.fa > color #3/D/E/F #335C71 > color #1/D/I/L #667255 > select #1/C,G,K:36 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/C,G,K:36-78 975 atoms, 996 bonds, 129 residues, 1 model selected > select add #1 11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected > select subtract #1 Nothing selected > color byattribute seq_conservation 23091 atoms, 2984 residues, atom seq_conservation range -0.918 to 100 > color #1/C/G/K byattr seq_conservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byattribute #1/C/G/K seq_conservation Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces' or a keyword > color byattribute seq_conservation #1/C/G/K 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation palette cyanmaroon range -0.918 0.918 > #1/C/G/K Invalid ""range"" argument: Expected 2-tuple of numbers or 'full' > color byattribute seq_conservation palette cyanmaroon range -0.918,0.918 > #1/C/G/K Expected a keyword > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,0.918 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > hide #!3 models > show #3/D/I/L ribbons > show #1/D/I/L ribbons > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,20 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,5 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,10 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,12 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,1 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,3 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,3 noValueColor grey 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,10 noValueColor grey 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,8 noValueColor grey 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,7 noValueColor grey 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,6 noValueColor grey 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #1/C/G/K palette cyanmaroon range > -0.918,5 noValueColor grey 3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100 > hide #!1 models > show #!3 models > hide #3/G/I/K ribbons > hide #3/J/H/L ribbons > color byattribute seq_conservation #3/A/B/C palette cyanmaroon range > -0.918,5 noValueColor grey 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette pastel2-8 range -0.918,5 > noValueColor grey 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 Fetching palette PuBu-5range from https://www.colourlovers.com/api/palettes?keywords=PuBu-5range&format=json&numResults=100 Could not find palette PuBu-5range at COLOURlovers.com using keyword search > color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,5 > noValueColor grey 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,5 > noValueColor white 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,10 > noValueColor white 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,3 > noValueColor white 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,3 > noValueColor white key true > key pubu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true > ui mousemode right ""color key"" 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > key ^pubu :3.00 :2.02 :1.04 :0.06 :-0.92 > key pubu :-0.92 :0.06 :1.04 :2.02 :3.00 > key ^pubu :3.00 :2.02 :1.04 :0.06 :-0.92 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,3 > noValueColor white key true > key ylgnbu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,2 > noValueColor white key true > key ylgnbu :-0.92 :-0.19 :0.54 :1.27 :2.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,1 > noValueColor white key true > key ylgnbu :-0.92 :-0.44 :0.04 :0.52 :1.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range > -0.918,100 noValueColor white key true > key ylgnbu :0 :24 :50 :75 :100 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,10 > noValueColor white key true > key ylgnbu :-0.9 :1.8 :4.5 :7.3 :10.0 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,3 > noValueColor white key true > key ylgnbu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,3 > noValueColor grey key true > key ylgnbu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color #3/A/B/C:1-52 grey > color #3/A:1-52 grey > color #3/B:1-52 grey > color #3/C:1-52 grey > color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,1 > noValueColor grey key true > key ylgnbu :-0.92 :-0.44 :0.04 :0.52 :1.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C range -0.918,1 noValueColor grey > key true > key blue-white-red :-0.92 :0.04 :1.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A range -0.918,1 noValueColor grey key > true > key blue-white-red :-0.92 :0.04 :1.00 showTool true 1199 atoms, 157 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A range -0.500,0.500 noValueColor grey > key true > key blue-white-red :-0.5 :0.0 :0.5 showTool true 1199 atoms, 157 residues, atom seq_conservation range -0.918 to 100 Fetching palette YlOrBr-5novalue from https://www.colourlovers.com/api/palettes?keywords=YlOrBr-5novalue&format=json&numResults=100 Could not find palette YlOrBr-5novalue at COLOURlovers.com using keyword search > color byattribute seq_conservation #3/A range -0.500,0.500 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.50 :-0.25 :0.00 :0.25 :0.50 showTool true 1199 atoms, 157 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C range -0.500,0.500 palette > ylorbr-5 noValueColor grey key true > key ylorbr :-0.50 :-0.25 :0.00 :0.25 :0.50 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C range -0.500,7 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.50 :1.38 :3.25 :5.12 :7.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C range -0.500,10 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.5 :2.1 :4.8 :7.4 :10.0 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C range -0.500,18 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.5 :4.1 :8.8 :13.4 :18.0 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > color byattribute seq_conservation #3/A/B/C range -0.500,6 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.50 :1.12 :2.75 :4.38 :6.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100 > open /Users/tgewering/Downloads/EBOV_MARV_GP1_global_align.fa Summary of feedback from opening /Users/tgewering/Downloads/EBOV_MARV_GP1_global_align.fa --- notes | Alignment identifier is EBOV_MARV_GP1_global_align.fa Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to MARV_GP1 (0 aa) with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to MARV_GP1 (0 aa) with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to MARV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 (0 aa) with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 (0 aa) with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment EBOV_MARV_GP1_global_align.fa Opened 2 sequences from EBOV_MARV_GP1_global_align.fa > select #1/C,G,K:36-37 39 atoms, 36 bonds, 6 residues, 1 model selected > select #1/C,G,K:36-37 #3/A-C:52-53 78 atoms, 72 bonds, 12 residues, 2 models selected EBOV_MARV_GP1_global_align.fa [ID: EBOV_MARV_GP1_global_align.fa] region MARV_GP1 (0 aa)..EBOV_GP1 (0 aa) [21-22] RMSD: 1.961 > color byattribute seq_conservation #3/A/B/C range -0.500,6 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.50 :1.12 :2.75 :4.38 :6.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,20 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.9 :4.3 :9.5 :14.8 :20.0 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,5 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.92 :0.56 :2.04 :3.52 :5.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,5 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.92 :0.56 :2.04 :3.52 :5.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,1 palette ylorbr-5 > noValueColor grey key true > key ylorbr :-0.92 :-0.44 :0.04 :0.52 :1.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > key colorTreatment distinct Fetching compressed palette GIant from https://www.colourlovers.com/api/palettes?keywords=GIant&format=json&numResults=100 Could not find palette GIant at COLOURlovers.com using keyword search > color name taupe #483C32 Color 'taupe' is opaque: rgb(28.2%, 23.5%, 19.6%) hex: #483c32 > color name copper #B87333 Color 'copper' is opaque: rgb(72.2%, 45.1%, 20%) hex: #b87333 > color name tan #D2B48C Can not override builtin color > color byattribute seq_conservation #3/A/B/C range -0.918,1 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:0.04 tan:1.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > select #1/C,G,K:141 12 atoms, 9 bonds, 3 residues, 1 model selected > select #1/C,G,K:141-148 210 atoms, 216 bonds, 24 residues, 1 model selected > select #3/A-C:157 12 atoms, 9 bonds, 3 residues, 1 model selected > select #3/A-C:157-164 210 atoms, 216 bonds, 24 residues, 1 model selected > select #3/A-C:156 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/C,G,K:139-140 #3/A-C:155-156 120 atoms, 120 bonds, 12 residues, 2 models selected EBOV_MARV_GP1_global_align.fa [ID: EBOV_MARV_GP1_global_align.fa] region MARV_GP1 (0 aa)..EBOV_GP1 (0 aa) [124-125] RMSD: 0.364 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3171, in run self._process_keyword_arguments(final, prev_annos) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3088, in _process_keyword_arguments value, text = self._parse_arg(anno, text, session, final) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2780, in _parse_arg value, replacement, rest = annotation.parse(text, session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 958, in parse return anno.parse(text, session) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 855, in parse token, text, rest = next_token(text, convert=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2056, in next_token token = unescape(token) ^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 1933, in unescape return unescape_with_index_map(text)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 1962, in unescape_with_index_map if text[index + count] not in ""01234567"": ~~~~^^^^^^^^^^^^^^^ IndexError: string index out of range IndexError: string index out of range File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 1962, in unescape_with_index_map if text[index + count] not in ""01234567"": ~~~~^^^^^^^^^^^^^^^ See log for complete Python traceback. > color byattribute seq_conservation #3/A/B/C range -0.918,15 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.9 #b87333:7.0 tan:15.0 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,2 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:0.54 tan:2.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,1 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:0.04 tan:1.00 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #3/A/B/C range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09 > select add #3 11559 atoms, 11875 bonds, 3 pseudobonds, 1502 residues, 3 models selected > select subtract #3 66 atoms, 69 bonds, 6 residues, 1 model selected > hide #!3 models > show #!1 models > color byattribute seq_conservation #1/D/I/L range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 2814 atoms, 350 residues, atom seq_conservation range 100 to 100 > undo > color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > open /Users/tgewering/Downloads/EBOV_MARV_GP1_clustal.aln Summary of feedback from opening /Users/tgewering/Downloads/EBOV_MARV_GP1_clustal.aln --- notes | Alignment identifier is EBOV_MARV_GP1_clustal.aln Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to MARV_GP1 with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to MARV_GP1 with 0 mismatches Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to MARV_GP1 with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 with 0 mismatches Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment EBOV_MARV_GP1_clustal.aln Opened 2 sequences from EBOV_MARV_GP1_clustal.aln > color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,7 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:3.04 tan:7.00 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,2 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:0.54 tan:2.00 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,1 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.92 #b87333:0.04 tan:1.00 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,0.2 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.918 #b87333:-0.359 tan:0.200 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color byattribute seq_conservation #1/C/G/K range -0.918,0.1 palette > taupe:copper:tan noValueColor grey key true > key #483c32:-0.918 #b87333:-0.409 tan:0.100 showTool true 3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09 > color similarity matrix blosum62 threshold 0.5 Unknown command: sequence color similarity matrix blosum62 threshold 0.5 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/H #3/G #3/I #3/K Alignment identifier is 1 ===== Log before crash end ===== Log: Startup Messages --- warning | No presets found in custom preset folder /Users/tgewering/Desktop/ChimeraX_preferences note | available bundle cache has not been initialized yet > set bgColor white > lighting soft > show cartoons > hide atoms > cartoon style thickness 1.2 > graphics silhouettes true UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: MPHE3LL/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 23 days, 22 hours, 18 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal EA244WMi: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported ASUS VE278: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX