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Opened 5 years ago
Last modified 5 years ago
#3718 assigned defect
Corrupted settings file?
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-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.
How to cite UCSF ChimeraX
> open
> /Users/carina/Documents/mann/00_manuscript/20200407_SI_figure_2/cryosparc_J28_reference_map/cryosparc_P46_J28_008_volume_map.mrc
Opened cryosparc_P46_J28_008_volume_map.mrc, grid size 200,200,200, pixel
1.06, shown at level 0.39, step 1, values float32
> open "/Users/carina/Documents/mann/00_manuscript/00_REVISIONS/00_PDB
> SUBMISSION/submission/postprocess_masked_J216.mrc"
Opened postprocess_masked_J216.mrc, grid size 200,200,200, pixel 1.06, shown
at level 0.0237, step 1, values float32
> hide #!1 models
> select #1
2 models selected
> close
> open "/Users/carina/Documents/mann/00_manuscript/00_REVISIONS/00_PDB
> SUBMISSION/submission/postprocess_masked_J216.mrc"
Opened postprocess_masked_J216.mrc, grid size 200,200,200, pixel 1.06, shown
at level 0.0237, step 1, values float32
> set bgColor white
> save session
> /Users/carina/Documents/mann/chimeraX/20200915_chimera_movie.cxs
> surface dust #1 size 10
> volume #1 level 0.182
> volume #1 level 0.02215
> volume #1 level 0.02508
> volume #1 level 0.02215
> volume #1 level 0.02288
> volume #1 level 0.02508
> open "/Users/carina/LRZ Sync+Share/cGAS_Nuc_manuscript/maps/final_cgas.pdb"
Summary of feedback from opening /Users/carina/LRZ
Sync+Share/cGAS_Nuc_manuscript/maps/final_cgas.pdb
---
warnings | Ignored bad PDB record found on line 3070
TER
Ignored bad PDB record found on line 5758
TER
Ignored bad PDB record found on line 8461
TER
Ignored bad PDB record found on line 9270
TER
Ignored bad PDB record found on line 9996
TER
7 messages similar to the above omitted
Chain information for final_cgas.pdb #2
---
Chain | Description
I | No description available
J | No description available
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
i | No description available
> set bgColor white
> lighting shadows false
> hide #2 models
> volume #1 level 0.02288
> volume #1 level 0.02288
> volume #1 level 0.02655
> volume #1 level 0.02215
> hide atoms
> show cartoons
> show #2 models
> color /a #70A9FA
> color /I #708090
> color /J #708090
> color /b #D3D3D3
> color /c #D3D3D3
> color /d #D3D3D3
> color /e #D3D3D3
> color /f #D3D3D3
> color /g #D3D3D3
> color /h #D3D3D3
> color /i #D3D3D3
> hide #!1 models
> color zone #1 near #2 distance 4
> show #!1 models
> hide #2 models
> lighting simple
> lighting soft
> lighting soft
> volume #1 level 0.02435
> set silhouettes true
> set silhouettes false
> color /b #FFD700
> color /c #B22222
> color /f #FFD700
> color /g #B22222
> color zone #1 near #2 distance 4
> volume #1 level 0.02655
> volume #1 level 0.02435
> hide #!1 models
> show #2 models
> cartoon style width 1.5 thickness 0.3
> cartoon style /I width 0.8 thickness 0.8
> lighting model #1 depthCue true
> show #!1 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #!1 models
> show #2 models
> save session
> /Users/carina/Documents/mann/chimeraX/20200915_chimera_movie.cxs
> nucleotides stubs
> nucleotides ladder
> hide /I cartoons
> show /I atoms
> hide /J cartoons
> show /J atoms
> show /I cartoons
> show /J cartoons
> nucleotides fill
> style nucleic stick
Changed 5389 atom styles
> nucleotides ladder
> nucleotides fill
> show #!1 models
> hide #!1 models
> hide #2 models
> show #!1 models
> windowsize 840 630
> windowsize 840 630
> set maxFrameRate 25
> view name side
> view name top
> view side
> view name close
> view side
> roll y 20 150 rock 150
> wait 150
> set maxFrameRate 25
Unknown command: View side
> movie record supersample 3
> wait 10
> roll y 20 150 rock 150
> wait 150
> wait 10
Unknown command: View top
> movie record supersample 3
Already recording a movie
> wait 10
> view side
> movie record supersample 3
Already recording a movie
> wait 10
> roll y 20 150 rock 150
> wait 150
> wait 10
> view top
> wait 10
> view side
> view top 40
> wait 40
> view side
> view top 30
> wait 30
> view side
> view top 30
> wait 30
> wait 10
Unknown command: View side 20; wait 20
> view side
> view top 30
> wait 30
> wait 10
> view side 20
> wait 20
> view top 30
> wait 30
> wait 10
> view side 20
> wait 20
> view close 30
> wait 30
> save session
> /Users/carina/Documents/mann/chimeraX/20200915_chimera_movie.cxs
> perframe "trans #1 $1 targ s" ranges 100,0 frames 100
> show #2 models
> perframe "trans #1 $1 targ s" ranges 100,10 frames 100
> perframe "trans #1 $1 targ s" ranges 0,10 frames 100
> perframe "trans #1 $1 targ s" ranges 0,100 frames 100
> perframe "trans #1 $1 targ s" ranges 0,120 frames 100
> perframe "trans #1 $1 targ s" ranges 100,10 frames 100
> hide #2 models
> view side
> wait 10
> roll y 20 150 rock 150
> wait 150
> wait 10
> view top 30
> wait 30
> wait 10
> view side 20
> wait 20
> view close 30
> wait 30
> wait 10
> perframe "trans #1 $1 targ s" ranges 100,0 frames 100
> show #2 models
> set bgColor white
> lighting shadows false
> lighting soft
> set silhouettes false
> hide #2 models
> roll y 20 100 rock 100
> wait 100
> roll y 20 80 rock 80
> wait 80
> save session
> /Users/carina/Documents/mann/chimeraX/20200915_chimera_movie.cxs
> show #2 models
> hide #!1 models
> select #1/a:241
Nothing selected
Unknown command: Show sel atoms
> select #1/a:240
Nothing selected
Unknown command: Show sel atoms
> select #1/a:341
Nothing selected
Unknown command: Show sel atoms
> select #1/a:342
Nothing selected
Unknown command: Show sel atoms
> select #1/a:317
Nothing selected
Unknown command: Show sel atoms
> select #1/a:316
Nothing selected
Unknown command: Show sel atoms
> select #1/a:241
Nothing selected
> select #2/a:241
11 atoms, 10 bonds, 1 model selected
Expected a keyword
> select #2/a:241
11 atoms, 10 bonds, 1 model selected
Unknown command: Show sel atoms
> select #2/a:240
9 atoms, 8 bonds, 1 model selected
Unknown command: Show sel atoms
> select #2/a:341
11 atoms, 10 bonds, 1 model selected
Unknown command: Show sel atoms
> select #2/a:342
11 atoms, 10 bonds, 1 model selected
Unknown command: Show sel atoms
> select #2/a:317
6 atoms, 5 bonds, 1 model selected
Unknown command: Show sel atoms
> select #2/a:316
4 atoms, 3 bonds, 1 model selected
Unknown command: Show sel atoms
Expected a keyword
> select #2/a:241
11 atoms, 10 bonds, 1 model selected
> show sel atoms
> select #2/a:240
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> select #2/a:341
11 atoms, 10 bonds, 1 model selected
> show sel atoms
> select #2/a:342
11 atoms, 10 bonds, 1 model selected
> show sel atoms
> select #2/a:317
6 atoms, 5 bonds, 1 model selected
> show sel atoms
> select #2/a:316
4 atoms, 3 bonds, 1 model selected
> show sel atoms
Expected a keyword
Expected a keyword
Expected a keyword
Expected a keyword
Expected a keyword
> name cGAS-resi #2/a:241,240,222,341,342,337,316,317
> color cGAS-resi byhetero
> style cGAS-resi stick
Changed 74 atom styles
> select #2/a:222
11 atoms, 10 bonds, 1 model selected
> name cGAS-resi #2/a:241,240,222,341,342,337,316,317
> color cGAS-resi byhetero
> style cGAS-resi stick
Changed 74 atom styles
> name cGAS-resi #2/a:222,240,241,316,317,337,341,342
> color cGAS-resi byhetero
> style cGAS-resi stick
Changed 74 atom styles
> color cGAS-resi byhetero
> style cGAS-resi stick
Changed 74 atom styles
> select #2/a:241
11 atoms, 10 bonds, 1 model selected
> select #2/a:222
11 atoms, 10 bonds, 1 model selected
> select #2/a:240
9 atoms, 8 bonds, 1 model selected
> select #2/a:316
4 atoms, 3 bonds, 1 model selected
> select #2/a:317
6 atoms, 5 bonds, 1 model selected
> select #2/a:337
11 atoms, 10 bonds, 1 model selected
> select #2/a:341
11 atoms, 10 bonds, 1 model selected
> select #2/a:342
11 atoms, 10 bonds, 1 model selected
> select #2/a:222
11 atoms, 10 bonds, 1 model selected
> style sel stick
Changed 11 atom styles
> style #2/a:222 stick
Changed 11 atom styles
> select /a:241@CG
1 atom, 1 model selected
> undo
> undo
> undo
> undo
> undo
> select clear
> select /a:222
11 atoms, 10 bonds, 1 model selected
> style sel stick
Changed 11 atom styles
Expected ',' or a keyword
> show #2 atoms
> hide #2 atoms
> style #2/a:222 stick
Changed 11 atom styles
> show #2/a:222 atoms
> hide #2 atoms
> select clear
> show #2/a:222 atoms
> show #2/a:240 atoms
> show #2/a:241 atoms
> show #2/a:316 atoms
> show #2/a:317 atoms
> show #2/a:337 atoms
> show #2/a:341 atoms
> show #2/a:342 atoms
> show #2/b:71 atoms
> show #2/b:71 atoms
> show #2/b:61 atoms
> show #2/b:64 atoms
> show #2/b:90 atoms
> hide #!1 models
> show #2/b:71 atoms
> show #2/b:61 atoms
> show #2/b:64 atoms
> show #2/b:90 atoms
> hide #!1 models
> show #2/b:71 atoms
> show #2/b:61 atoms
> show #2/b:64 atoms
> show #2/b:90 atoms
> show #2/b:91 atoms
> show #2/b:92 atoms
> show #2/c:49 atoms
> show #2/c:51 atoms
Expected a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> style stick
Changed 13959 atom styles
> style stick
Changed 13959 atom styles
> color byhetero
> interfaces ~solvent
24 buried areas: J I 6057, f g 2501, b c 2486, d i 2451, h e 2123, J d 699, b
d 695, I d 675, d h 599, a b 532, g i 491, c e 485, J b 452, b i 444, I b 430,
J f 418, I f 412, I c 409, I h 390, a c 379, J e 362, I i 348, f e 315, J c
303
> hbonds
1190 hydrogen bonds found
> hbonds
1190 hydrogen bonds found
> hide hbonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select /b:36
9 atoms, 8 bonds, 1 model selected
> select clear
> select /a:241@CZ
1 atom, 1 model selected
> select /b:92@CD
1 atom, 1 model selected
> select /b:90@CG
1 atom, 1 model selected
> toolshed show H-Bonds
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x12fb6cf10>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
> hbonds sel
5 hydrogen bonds found
> ~hbonds
> hbonds sel
5 hydrogen bonds found
> toolshed show H-Bonds
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x16436c850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__
self._session, value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string
new_value = self.convert_from_string(session, str_value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string
return self.from_str(str_value)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 91, in literal_eval
return _convert(node_or_string)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 90, in _convert
return _convert_signed_num(node)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 63, in _convert_signed_num
return _convert_num(node)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 55, in _convert_num
raise ValueError('malformed node or string: ' + repr(node))
ValueError: malformed node or string: <_ast.Call object at 0x12fb67050>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 179, in __getattr__
return self._cur_settings[name]
KeyError: '_name'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py", line 49, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py", line 362, in get_command
self.__settings.save(settings=saveables)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 362, in __setattr__
(self._name, name))
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
AttributeError: _name
AttributeError: _name
File
"/private/var/folders/ny/lfnzjkld3bq5wtbysk5bwt5w0000gn/T/AppTranslocation/8A6D907C-667F-4CB5-8DFE-760064A0313A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 181, in __getattr__
raise AttributeError(name)
See log for complete Python traceback.
OpenGL version: 4.1 ATI-2.11.22
OpenGL renderer: AMD Radeon Pro 570X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Change History (1)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Corrupted settings file? |
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