id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7433 Destruction of status bar during session restore: wrapped C/C++ object of type QScreen has been deleted maru.jaimegarza@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/maru/Desktop/Models/from40_148_isolde_v10.pdb Chain information for from40_148_isolde_v10.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > hide atoms > show cartoons > select /B:96 12 atoms, 11 bonds, 1 residue, 1 model selected > select add /A:14 32 atoms, 31 bonds, 2 residues, 1 model selected > select add /F:45 54 atoms, 52 bonds, 3 residues, 1 model selected > select add /D:401 73 atoms, 70 bonds, 4 residues, 1 model selected > select add /C:656 89 atoms, 85 bonds, 5 residues, 1 model selected > select add /F:224 111 atoms, 106 bonds, 6 residues, 1 model selected > select add /G:588 131 atoms, 126 bonds, 7 residues, 1 model selected > select up 2227 atoms, 2231 bonds, 132 residues, 1 model selected > select up 26741 atoms, 26967 bonds, 1637 residues, 1 model selected > select add /H:440 26763 atoms, 26988 bonds, 1638 residues, 1 model selected > select up 26872 atoms, 27100 bonds, 1644 residues, 1 model selected > select up 28125 atoms, 28365 bonds, 1722 residues, 1 model selected > color sel dark gray > select clear Drag select of 122 residues > select up 2131 atoms, 2150 bonds, 130 residues, 1 model selected > color sel #b8b0ddff > select clear Drag select of 210 residues > select up 3865 atoms, 3909 bonds, 248 residues, 1 model selected > select up 7326 atoms, 7408 bonds, 459 residues, 1 model selected > select up 35535 atoms, 35855 bonds, 2189 residues, 1 model selected > select down 7326 atoms, 7408 bonds, 459 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium purple > select clear Drag select of 121 residues > select up 2131 atoms, 2150 bonds, 130 residues, 1 model selected > color sel #b8b0ddff > select clear > open /Users/maru/Downloads/1wao_cat.pdb Summary of feedback from opening /Users/maru/Downloads/1wao_cat.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ALA 3 28 LYS 3 32 1 5 Start residue of secondary structure not found: HELIX 2 2 ALA 3 35 LYS 3 42 1 8 Start residue of secondary structure not found: HELIX 3 3 TYR 3 44 PHE 3 50 1 7 Start residue of secondary structure not found: HELIX 4 4 ILE 3 63 TYR 3 72 1 10 Start residue of secondary structure not found: HELIX 5 5 CYS 3 77 ALA 3 85 1 9 4 messages similar to the above omitted Cannot find LINK/SSBOND residue MN (601 ) Cannot find LINK/SSBOND residue MN (601 ) Cannot find LINK/SSBOND residue MN (601 ) Cannot find LINK/SSBOND residue MN (601 ) Cannot find LINK/SSBOND residue MN (602 ) 2 messages similar to the above omitted 1wao_cat.pdb title: PP5 structure [more info...] Chain information for 1wao_cat.pdb #2 --- Chain | Description 3 | serine/threonine protein phosphatase 5 > mmaker #2 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 from40_148_isolde_v10.pdb, chain E (#1) with 1wao_cat.pdb, chain 3 (#2), sequence alignment score = 2029.5 RMSD between 262 pruned atom pairs is 1.137 angstroms; (across all 323 pairs: 1.890) > select #2/3:482 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 166 atoms, 170 bonds, 23 residues, 1 model selected > select up 2717 atoms, 2781 bonds, 341 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium purple > select clear > select add #2/3:499 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/3:497 9 atoms, 7 bonds, 2 residues, 1 model selected > select add #2/3:498 14 atoms, 11 bonds, 3 residues, 1 model selected > select add #2/3:496 22 atoms, 18 bonds, 4 residues, 1 model selected > select add #2/3:495 31 atoms, 26 bonds, 5 residues, 1 model selected > select add #2/3:494 39 atoms, 33 bonds, 6 residues, 1 model selected > select add #2/3:493 47 atoms, 40 bonds, 7 residues, 1 model selected > select add #2/3:492 54 atoms, 46 bonds, 8 residues, 1 model selected > select add #2/3:491 62 atoms, 53 bonds, 9 residues, 1 model selected > select add #2/3:490 67 atoms, 57 bonds, 10 residues, 1 model selected > select add #2/3:488 72 atoms, 61 bonds, 11 residues, 1 model selected > select add #2/3:489 84 atoms, 73 bonds, 12 residues, 1 model selected > select add #2/3:487 92 atoms, 80 bonds, 13 residues, 1 model selected > select add #2/3:486 99 atoms, 87 bonds, 14 residues, 1 model selected > select subtract #2/3:486 92 atoms, 80 bonds, 13 residues, 1 model selected > select subtract #2/3:487 84 atoms, 73 bonds, 12 residues, 1 model selected > select subtract #2/3:488 79 atoms, 69 bonds, 11 residues, 1 model selected > color sel #ff2600ff > select clear > ui tool show ""Side View"" > ui tool show ""Side View"" > select #2/3:484 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 166 atoms, 170 bonds, 23 residues, 1 model selected > select up 2717 atoms, 2781 bonds, 341 residues, 1 model selected > select subtract #2/3:499 2712 atoms, 2777 bonds, 340 residues, 1 model selected > select subtract #2/3:498 2707 atoms, 2773 bonds, 339 residues, 1 model selected > select subtract #2/3:497 2703 atoms, 2770 bonds, 338 residues, 1 model selected > select subtract #2/3:496 2695 atoms, 2763 bonds, 337 residues, 1 model selected > select add #1/C:652 2717 atoms, 2784 bonds, 338 residues, 2 models selected > select subtract #1/C:652 2695 atoms, 2763 bonds, 337 residues, 1 model selected > select subtract #2/3:492 2688 atoms, 2757 bonds, 336 residues, 1 model selected > select subtract #2/3:491 2680 atoms, 2750 bonds, 335 residues, 1 model selected > select subtract #2/3:493 2672 atoms, 2743 bonds, 334 residues, 1 model selected > select subtract #2/3:494 2664 atoms, 2736 bonds, 333 residues, 1 model selected > select subtract #2/3:495 2655 atoms, 2728 bonds, 332 residues, 1 model selected > select subtract #2/3:490 2650 atoms, 2724 bonds, 331 residues, 1 model selected > select subtract #2/3:489 2638 atoms, 2712 bonds, 330 residues, 1 model selected > select subtract #2/3:488 2633 atoms, 2708 bonds, 329 residues, 1 model selected > select subtract #2/3:487 2625 atoms, 2701 bonds, 328 residues, 1 model selected > select subtract #2/3:486 2618 atoms, 2694 bonds, 327 residues, 1 model selected > select subtract #2/3:485 2609 atoms, 2686 bonds, 326 residues, 1 model selected > select add #2/3:485 2618 atoms, 2694 bonds, 327 residues, 1 model selected > select subtract #2/3:485 2609 atoms, 2686 bonds, 326 residues, 1 model selected > select subtract #2/3:484 2602 atoms, 2680 bonds, 325 residues, 1 model selected > select subtract #2/3:483 2594 atoms, 2673 bonds, 324 residues, 1 model selected > select subtract #2/3:482 2587 atoms, 2666 bonds, 323 residues, 1 model selected > cartoon hide sel > select #1/G:609 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 163 atoms, 162 bonds, 10 residues, 1 model selected > select up 1723 atoms, 1743 bonds, 106 residues, 1 model selected > color sel #cf3a5eff > select #1/H:451 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 318 atoms, 320 bonds, 20 residues, 1 model selected > select up 1384 atoms, 1398 bonds, 85 residues, 1 model selected > color sel #cf3a5eff > select clear > save /Users/maru/Desktop/grayALL_PP5color.png width 847 height 623 > supersample 4 transparentBackground true > open /Users/maru/Downloads/6xlg.pdb 6xlg.pdb title: Full-length HSC82 In complex with two AHA1 CTD In the presence of atpgammas [more info...] Chain information for 6xlg.pdb #3 --- Chain | Description A B | atp-dependent molecular chaperone HSC82 C D | activator OF HSP90 atpase protein 1 Non-standard residues in 6xlg.pdb #3 --- AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) K — potassium ion MG — magnesium ion > open /Users/maru/Desktop/Models/from40_148_isolde_v10.pdb Chain information for from40_148_isolde_v10.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > view clip false > mmaker #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 from40_148_isolde_v10.pdb, chain D (#1) with 6xlg.pdb, chain B (#3), sequence alignment score = 1453.7 RMSD between 319 pruned atom pairs is 1.071 angstroms; (across all 397 pairs: 1.566) > close #4 Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C Alignment identifier is 1/D Alignment identifier is 1/E Alignment identifier is 1/F Alignment identifier is 1/G Alignment identifier is 1/H Alignment identifier is 2/3 Alignment identifier is 1 Alignment identifier is 2 > select #3/A-B:282 18 atoms, 16 bonds, 2 residues, 1 model selected > select #3/A-B:282 18 atoms, 16 bonds, 2 residues, 1 model selected > select #3/A-B:281 14 atoms, 12 bonds, 2 residues, 1 model selected > select #3/A-B:281 14 atoms, 12 bonds, 2 residues, 1 model selected > open /Users/maru/Downloads/2cg9.pdb 2cg9.pdb title: Crystal structure of an HSP90-SBA1 closed chaperone complex [more info...] Chain information for 2cg9.pdb #4 --- Chain | Description A B | atp-dependent molecular chaperone HSP82 X Y | Co-chaperone protein SBA1 Non-standard residues in 2cg9.pdb #4 --- ATP — adenosine-5'-triphosphate > mmaker #4 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 from40_148_isolde_v10.pdb, chain D (#1) with 2cg9.pdb, chain B (#4), sequence alignment score = 1342.4 RMSD between 331 pruned atom pairs is 1.017 angstroms; (across all 402 pairs: 1.785) > close #3 > select #4 11906 atoms, 12124 bonds, 9 pseudobonds, 1459 residues, 2 models selected Alignment identifier is 1 Alignment identifier is 2 > select clear > select #4/A-B:282 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:282 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel red > select #4/A-B:297 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:297-298 28 atoms, 26 bonds, 4 residues, 1 model selected > select #4/A-B:297 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:297 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel red > select #4/B:334 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/B:334 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > select #4/A-B:379 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel red > select #4/A-B:450 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:450 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel red > hide #!4 models > show #!4 models > hide #2 models > hide #1 models > select #4/A-B:456 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:456 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel red > select #4/A-B:485 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:485 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel red > select #4/A-B:533 14 atoms, 12 bonds, 2 residues, 1 model selected > select #4/A-B:533 14 atoms, 12 bonds, 2 residues, 1 model selected > color sel red > color sel red > show #2 models > hide #2 models > show #1 models > select add #1/G:609 24 atoms, 21 bonds, 3 residues, 2 models selected > select add #1/F:39 48 atoms, 44 bonds, 4 residues, 2 models selected > select up 1178 atoms, 1180 bonds, 79 residues, 2 models selected > select up 16016 atoms, 16244 bonds, 1594 residues, 2 models selected > select down 1178 atoms, 1180 bonds, 79 residues, 2 models selected > select add #1/G:589 1195 atoms, 1196 bonds, 80 residues, 2 models selected > select down 1195 atoms, 1196 bonds, 80 residues, 2 models selected > select up 1329 atoms, 1331 bonds, 88 residues, 2 models selected > select up 16016 atoms, 16244 bonds, 1594 residues, 2 models selected > select down 1329 atoms, 1331 bonds, 88 residues, 2 models selected > select add #1/G:571 1346 atoms, 1347 bonds, 89 residues, 2 models selected > select up 1605 atoms, 1610 bonds, 105 residues, 2 models selected > select up 16016 atoms, 16244 bonds, 1594 residues, 2 models selected > hide sel cartoons > show sel cartoons > select clear > select add #1/A:220 24 atoms, 23 bonds, 1 residue, 1 model selected > select add #1/F:39 48 atoms, 46 bonds, 2 residues, 1 model selected > select add #1/G:637 67 atoms, 64 bonds, 3 residues, 1 model selected > select add #1/H:463 84 atoms, 80 bonds, 4 residues, 1 model selected > select up 1412 atoms, 1418 bonds, 83 residues, 1 model selected > select up 10847 atoms, 10946 bonds, 667 residues, 1 model selected > hide sel cartoons > select add #1/C:278 10859 atoms, 10957 bonds, 668 residues, 1 model selected > select up 10895 atoms, 10993 bonds, 670 residues, 1 model selected > select up 17835 atoms, 17991 bonds, 1089 residues, 1 model selected > hide sel cartoons > select add #1/B:12 17850 atoms, 18005 bonds, 1090 residues, 1 model selected > select add #1/B:167 17874 atoms, 18028 bonds, 1091 residues, 1 model selected > select up 18005 atoms, 18161 bonds, 1100 residues, 1 model selected > select up 21158 atoms, 21341 bonds, 1300 residues, 1 model selected > hide sel cartoons > select add #1/D:523 21175 atoms, 21357 bonds, 1301 residues, 1 model selected > select up 21319 atoms, 21503 bonds, 1310 residues, 1 model selected > select up 28125 atoms, 28365 bonds, 1722 residues, 1 model selected > hide sel cartoons > ui mousemode right label > label delete residues > label delete residues > label delete residues > label #4/A:456 > label #4/A:450 > label #4/B:652 > label #4/B:485 > label #4/B:533 > label #4/A:533 > label #4/B:282 > label #4/B:297 > label #4/A:297 > label #4/A:282 > ui mousemode right ""move label"" > ui mousemode right label > label delete residues > label #4/A:450 > label delete residues > label delete residues > label #4/A:456 > label #4/A:450 > label #4/A:485 > label #4/B:450 > label #4/A:533 > label #4/B:456 > ui mousemode right ""move label"" > save /Users/maru/Desktop/yHsp90_Phospho.png width 1094 height 623 > supersample 3 > select #4/A-B:485 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:485 12 atoms, 10 bonds, 2 residues, 1 model selected > color sel orange red > color sel magenta > save /Users/maru/Desktop/S485affectedByPpt1-.png width 1094 height 623 > supersample 3 > select #4/A-B:379 12 atoms, 10 bonds, 2 residues, 1 model selected > select #4/A-B:379 12 atoms, 10 bonds, 2 residues, 1 model selected > select #1 35535 atoms, 35855 bonds, 2189 residues, 1 model selected > hide #!4 models > show sel cartoons > select clear > select #1/G:608 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 163 atoms, 162 bonds, 10 residues, 1 model selected > select up 1723 atoms, 1743 bonds, 106 residues, 1 model selected > select up 35535 atoms, 35855 bonds, 2189 residues, 1 model selected > select down 1723 atoms, 1743 bonds, 106 residues, 1 model selected > select add #1/H:451 1740 atoms, 1759 bonds, 107 residues, 1 model selected > select up 2041 atoms, 2063 bonds, 126 residues, 1 model selected > select up 3107 atoms, 3141 bonds, 191 residues, 1 model selected > color sel dark gray > select clear > select add #1/C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 421 atoms, 421 bonds, 24 residues, 1 model selected > select up 6988 atoms, 7045 bonds, 422 residues, 1 model selected Alignment identifier is 1/C > select #1/C:452 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/C:452 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > select #1/A:220 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 54 atoms, 53 bonds, 3 residues, 1 model selected > select up 3429 atoms, 3456 bonds, 217 residues, 1 model selected Alignment identifier is 1/A > select #1/A:57 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:57 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > select #1/A:62 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:62 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:59 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:59-60 26 atoms, 25 bonds, 2 residues, 1 model selected > select #1/A:59 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:59 14 atoms, 13 bonds, 1 residue, 1 model selected > color sel red > select #1/A:62 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:62 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > select #1/A:84 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:84 14 atoms, 13 bonds, 1 residue, 1 model selected > color sel red > select #1/A:205 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:205 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > select #1/A:225 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:225 12 atoms, 11 bonds, 1 residue, 1 model selected > color sel red > select clear > save /Users/maru/Desktop/hHsp90B_Phospho.png width 1001 height 623 > supersample 3 > open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/manager.py"", line 252, in reset_state alignment._destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 603, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 652, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 474, in alignment_notification self.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 512, in delete ToolInstance.delete(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 154, in delete self.session.ui.remove_tool(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 345, in remove_tool self.main_window.remove_tool(tool_instance) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 725, in remove_tool tw._destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 2049, in _destroy self.__toolkit.destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 2189, in destroy sbar.destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/statusbar.py"", line 51, in destroy v.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 438, in delete self.make_current() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 99, in make_current qc = self._initialize_context() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) RuntimeError: wrapped C/C++ object of type QScreen has been deleted Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/manager.py"", line 252, in reset_state alignment._destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 603, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 652, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 474, in alignment_notification self.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 512, in delete ToolInstance.delete(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 154, in delete self.session.ui.remove_tool(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 345, in remove_tool self.main_window.remove_tool(tool_instance) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 725, in remove_tool tw._destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 2049, in _destroy self.__toolkit.destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 2189, in destroy sbar.destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/statusbar.py"", line 51, in destroy v.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 438, in delete self.make_current() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 99, in make_current qc = self._initialize_context() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) RuntimeError: wrapped C/C++ object of type QScreen has been deleted During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 261, in event _open_dropped_file(self.session, event.file()) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 1812, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 422, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 982, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 721, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/manager.py"", line 252, in reset_state alignment._destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 603, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 652, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 474, in alignment_notification self.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 512, in delete ToolInstance.delete(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 154, in delete self.session.ui.remove_tool(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 345, in remove_tool self.main_window.remove_tool(tool_instance) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 725, in remove_tool tw._destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 2049, in _destroy self.__toolkit.destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 2189, in destroy sbar.destroy() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/statusbar.py"", line 51, in destroy v.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 438, in delete self.make_current() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 99, in make_current qc = self._initialize_context() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) RuntimeError: wrapped C/C++ object of type QScreen has been deleted RuntimeError: wrapped C/C++ object of type QScreen has been deleted File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) See log for complete Python traceback. > open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 261, in event _open_dropped_file(self.session, event.file()) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 1812, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 422, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 982, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 721, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list ValueError: list.remove(x): x not in list File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) See log for complete Python traceback. > open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide_2.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 261, in event _open_dropped_file(self.session, event.file()) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 1812, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 422, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 982, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 721, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list ValueError: list.remove(x): x not in list File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) See log for complete Python traceback. > open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/wPeptide_2.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/dialog.py"", line 155, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 422, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 982, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 721, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list ValueError: list.remove(x): x not in list File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) See log for complete Python traceback. > open /Users/maru/Desktop/FigureStructureImages/Fig4_redo/fig4redo.cxs Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 679, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 261, in event _open_dropped_file(self.session, event.file()) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 1812, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/open_command/cmd.py"", line 422, in collated_open return func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 982, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 721, in restore self.reset() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/session.py"", line 529, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seq-view/tool.py"", line 507, in delete self.alignment.detach_viewer(self) File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) ValueError: list.remove(x): x not in list ValueError: list.remove(x): x not in list File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 379, in detach_viewer self.viewers.remove(viewer) See log for complete Python traceback. OpenGL version: 4.1 Metal - 71.7.1 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 4 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 11.6 (20G165) Kernel Version: Darwin 20.6.0 Time since boot: 16 days 21:52 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Resolution: 2880 x 1800 UI Looks like: 1440 x 900 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 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: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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: 0.29.21 decorator: 5.0.9 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: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Graphics duplicate Eric Pettersen all ChimeraX