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#3549 closed defect (fixed)
Old save-map GUI: 'NoneType' object has no attribute 'id_string'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-03-14) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.93 (2020-03-14) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped-MB.cxs format session Log from Sat Jul 25 18:55:59 2020UCSF ChimeraX version: 0.93 (2020-03-14) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs format session Log from Thu Jul 23 18:05:20 2020UCSF ChimeraX version: 0.93 (2020-03-14) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs Log from Thu Jul 23 17:35:00 2020UCSF ChimeraX version: 0.93 (2020-03-14) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps.pdb 6wps.pdb title: Structure of the sars-cov-2 spike glycoprotein In complex with the S309 neutralizing antibody fab fragment [more info...] Chain information for 6wps.pdb #1 --- Chain | Description A B E | sars-cov-2 spike glycoprotein C F H | S309 neutralizing antibody heavy chain D G L | S309 neutralizing antibody light chain Non-standard residues in 6wps.pdb #1 --- BMA — β-D-mannose FUC — α-L-fucose MAN — α-D-mannose NAG — N-acetyl-D-glucosamine Drag select of 28116 atoms, 84 pseudobonds, 1086 bonds > hide sel atoms > show sel cartoons > select clear > select /A:27-1140 7386 atoms, 7559 bonds, 26 pseudobonds, 2 models selected > select /C:2-124 937 atoms, 962 bonds, 1 model selected > select /D:2-105 706 atoms, 721 bonds, 2 pseudobonds, 2 models selected > select /C:2-124 937 atoms, 962 bonds, 1 model selected > select /D:2-105 706 atoms, 721 bonds, 2 pseudobonds, 2 models selected > select /A:27-1140 7386 atoms, 7559 bonds, 26 pseudobonds, 2 models selected > select : 332-532 3925 atoms, 4033 bonds, 24 pseudobonds, 2 models selected > color sel red > select ~sel 24191 atoms, 24797 bonds, 60 pseudobonds, 2 models selected > select /A 7723 atoms, 7921 bonds, 26 pseudobonds, 2 models selected > select /A:332-532 1305 atoms, 1341 bonds, 8 pseudobonds, 2 models selected > select /H:2-124 937 atoms, 962 bonds, 1 model selected > select /L:2-105 706 atoms, 721 bonds, 2 pseudobonds, 2 models selected > select /A, H, L 9366 atoms, 9604 bonds, 28 pseudobonds, 2 models selected > select ~sel 18750 atoms, 19226 bonds, 56 pseudobonds, 2 models selected > hide sel Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel cartoons > select : 332-532 3925 atoms, 4033 bonds, 24 pseudobonds, 2 models selected > color sel green Unknown command: select: 444-508 > select : 444-508 793 atoms, 811 bonds, 24 pseudobonds, 2 models selected > color sel tan > select clear > select : 343 24 atoms, 21 bonds, 1 model selected > color sel cyan > select clear > select : > 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505 232 atoms, 217 bonds, 1 model selected > color sel coral > color sel cyan > select clear Unknown command: select: 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505 Unknown command: select: 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505 > select : > 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505 445 atoms, 424 bonds, 6 pseudobonds, 2 models selected > color sel yellow > select : > 337,338,339,340,341,342,343,344,345,346,354,356,357,358,359,360,361,440,441,442,443,444 525 atoms, 522 bonds, 1 model selected > color sel hotpink > select clear > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs includeMaps true > select up Nothing selected > select up Nothing selected > select : > 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505 232 atoms, 217 bonds, 1 model selected > color sel cyan > select clear > select down Nothing selected > select > :143,144,145,146,147,148,150,152,158,245,246,247,248,249,250,251,256,257 51 atoms, 48 bonds, 1 model selected > select : > 143,144,145,146,147,148,150,152,158,245,246,247,248,249,250,251,256,257 51 atoms, 48 bonds, 1 model selected > select : > 417,453,455,456,473,475,476,486,487,489,493,495,496,498,500,501,502,505 232 atoms, 220 bonds, 1 model selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel white > select clear > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs includeMaps true > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs includeMaps true > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs includeMaps true opened ChimeraX session > select up Nothing selected > select : > 372,389,428,374,377,392,429,515,519,378,386,390,517,370,384,376,385,430,382,369,380 561 atoms, 549 bonds, 1 model selected > color sel gray > select clear > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs includeMaps true > color sel lightgray > select : > 372,389,428,374,377,392,429,515,519,378,386,390,517,370,384,376,385,430,382,369,380 561 atoms, 549 bonds, 1 model selected > color sel lightgray > select clear > color sel cornflowerblue > select : > 372,389,428,374,377,392,429,515,519,378,386,390,517,370,384,376,385,430,382,369,380 561 atoms, 549 bonds, 1 model selected > color sel cornflowerblue > select clear > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps-mapped.cxs includeMaps true opened ChimeraX session > select up Nothing selected > close session > open > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/6wps/6wps.pdb 6wps.pdb title: Structure of the sars-cov-2 spike glycoprotein In complex with the S309 neutralizing antibody fab fragment [more info...] Chain information for 6wps.pdb #1 --- Chain | Description A B E | sars-cov-2 spike glycoprotein C F H | S309 neutralizing antibody heavy chain D G L | S309 neutralizing antibody light chain Non-standard residues in 6wps.pdb #1 --- BMA — β-D-mannose FUC — α-L-fucose MAN — α-D-mannose NAG — N-acetyl-D-glucosamine Drag select of 28116 atoms, 84 pseudobonds, 1086 bonds > hide sel atoms > hide sel cartoons > show sel cartoons > select clear > delete /B,E > delete /C,F,D,G > delete /H,L Drag select of 8 pseudobonds, 145 residues Drag select of 26 pseudobonds, 955 residues > color sel tan > select clear > select : 332-532 1305 atoms, 1341 bonds, 8 pseudobonds, 2 models selected > color sel gray > select clear > select up Nothing selected > select : 332-532 1305 atoms, 1341 bonds, 8 pseudobonds, 2 models selected > color sel lightgray > select clear > select : 444-508 263 atoms, 269 bonds, 8 pseudobonds, 2 models selected > select : > 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505 76 atoms, 71 bonds, 1 model selected > color sel cyan > select : 346,444,446,447,448,449,450,452,483,484,485,490,494 59 atoms, 55 bonds, 2 pseudobonds, 2 models selected > color sel hotpink > select clear > select : > 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505 145 atoms, 138 bonds, 2 pseudobonds, 2 models selected > color sel forestgreen > select up 398 atoms, 405 bonds, 2 pseudobonds, 2 models selected > color sel green > select : > 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505 145 atoms, 138 bonds, 2 pseudobonds, 2 models selected > color sel yellow Drag select of > select : > 334,335,337,339,340,341,343,344,345,346,354,356,358,359,360,361,440,441,444,509 155 atoms, 146 bonds, 1 model selected > color sel cyan > select : > 369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,389,390,392,427,428,429,430,515,516,517,519 228 atoms, 230 bonds, 1 model selected > color sel cornflowerblue > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped.cxs includeMaps true > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped.cxs includeMaps true > close session > open > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/06-20/6vxx/6vxx.pdb 6vxx.pdb title: Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...] Chain information for 6vxx.pdb #1 --- Chain | Description A B C | sars-cov-2 spike glycoprotein Non-standard residues in 6vxx.pdb #1 --- NAG — N-acetyl-D-glucosamine > delete /B,C Drag select of 457 atoms, 22 pseudobonds, 972 residues, 450 bonds > hide sel atoms > select clear > select up Nothing selected > select : 444-508 309 atoms, 318 bonds, 8 pseudobonds, 2 models selected > select : 532 8 atoms, 7 bonds, 1 model selected > select : 332-532 1371 atoms, 1410 bonds, 8 pseudobonds, 2 models selected > color sel lightgray > select clear > select : 532 8 atoms, 7 bonds, 1 model selected Unknown command: colore sel red > color sel red > select clear > select up Nothing selected > select up Nothing selected > select : > 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505 105 atoms, 101 bonds, 1 model selected > color sel cyan > select : > 334,335,337,339,340,341,343,344,345,346,354,356,358,359,360,361,440,441,444,509 155 atoms, 146 bonds, 1 model selected > color sel orange > select clear > select : > 369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,389,390,392,427,428,429,430,515,516,517,519 232 atoms, 234 bonds, 1 model selected > color sel hotpink > select clear > select up Nothing selected > select : 346,444,446,447,448,449,450,452,483,484,485,490,494 77 atoms, 73 bonds, 2 pseudobonds, 2 models selected > color sel yellow > select clear > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped-MB.cxs includeMaps true > save /Users/munmunbhasin/Desktop/image1.png supersample 3 > save /Users/munmunbhasin/Desktop/image2.png supersample 3 > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped-MB.cxs includeMaps true opened ChimeraX session > select : > 403,405,406,409,415,416,417,420,421,453,455,456,457,458,459,460,473,474,475,476,477,486,487,489,490,493,494,495,496,498,500,501,502,503,505 186 atoms, 180 bonds, 2 pseudobonds, 2 models selected > color sel cornflowerblue > select : > 417,446,449,453,455,456,473,475,476,484,486,487,489,490,493,496,498,500,501,502,505 105 atoms, 101 bonds, 1 model selected > color sel cyan > select clear > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped-MB.cxs includeMaps true > save /Users/munmunbhasin/Desktop/image1.png supersample 3 > save /Users/munmunbhasin/Desktop/image2.png supersample 3 > save /Users/munmunbhasin/Desktop/image3.png supersample 3 > save session > /Users/munmunbhasin/Documents/WORK/MBU_WORK/My_data/8_covid19/07-20/epitopes- > compare/epitopes-mapped-MB.cxs includeMaps true Traceback (most recent call last): File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 935, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 651, in file_save_cb self.save_dialog.display(self, session) File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/savemap.py", line 53, in save self._map_menu.value.id_string) AttributeError: 'NoneType' object has no attribute 'id_string' AttributeError: 'NoneType' object has no attribute 'id_string' File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/savemap.py", line 53, in save self._map_menu.value.id_string) See log for complete Python traceback. Traceback (most recent call last): File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 935, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 651, in file_save_cb self.save_dialog.display(self, session) File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/savemap.py", line 53, in save self._map_menu.value.id_string) AttributeError: 'NoneType' object has no attribute 'id_string' AttributeError: 'NoneType' object has no attribute 'id_string' File "/private/var/folders/dt/2f7_8mfx4k750gb29zwk3b6m0000gn/T/AppTranslocation/975288A3-16DF-45E0-8256-A5DA734E2ABE/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/savemap.py", line 53, in save self._map_menu.value.id_string) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.8 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.
Change History (3)
comment:1 by , 5 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Old save-map GUI: 'NoneType' object has no attribute 'id_string' |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
comment:3 by , 5 years ago
| Reporter: | changed from to |
|---|
Hi Munmun,
This problem is fixed in the ChimeraX 1.0 release. If you are a user of ISOLDE you will have to wait to upgrade because a 1.9-compatible version of ISOLDE isn't available yet. If you don't use ISOLDE, go ahead and upgrade.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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See TracTickets
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Hi Munmun,
--Eric