Opened 5 years ago

Last modified 5 years ago

#4286 feedback defect

Problem saving clashes settings

Reported by: mks131@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core 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: 0.92 (2020-03-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.92 (2020-03-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ubcg90c/Downloads/Lin28B_NCP.pdb

Chain information for Lin28B_NCP.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D H | No description available  
E | No description available  
F | No description available  
G | No description available  
I | No description available  
J | No description available  
  

> open
> /Users/ubcg90c/Desktop/Lin28_nu/postprocess_masked_refined_pixelsize_align.mrc

Opened postprocess_masked_refined_pixelsize_align.mrc, grid size 376,376,376,
pixel 0.649, shown at level 0.00472, step 2, values float32  

> volume #2 level 0.008349

> toolshed show Clashes

> clashes

2 clashes  

> show atoms

> nucleotides stubs

> transparency 50

> nucleotides atoms

> style nucleic stick

Changed 5371 atom styles  

> style sphere

Changed 11363 atom styles  

> style sphere

Changed 11363 atom styles  

> style sphere

Changed 11363 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 5371 atom styles  

> style stick

Changed 11363 atom styles  

> volume #2 level 0.009905

> toolshed show Clashes

> clashes overlapCutoff 0.4

42 clashes  
Traceback (most recent call last):  
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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 0x137ac6ed0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/gui.py", line 570, in get_command  
self.settings.save(settings=saveables)  
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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 0x137ac6a90>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/gui.py", line 570, in get_command  
self.settings.save(settings=saveables)  
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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-3.10.16
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Problem saving clashes settings

comment:2 by Eric Pettersen, 5 years ago

Status: accepted → feedback

Hi Manoj,

Thanks for reporting this problem. Could you upgrade to the latest release (1.1.1) and see if the problem persists? There have been a lot of bug fixes since the release (0.92) that you are using. If you still get the problem, please send a session file from _just before_ using clashes. That will help me debug the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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