Opened 5 years ago

Closed 5 years ago

#3945 closed defect (duplicate)

Error saving settings

Reported by: s1960571@… 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: 0.93 (2020-03-12)
Description
Trying to find contacts

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.93 (2020-03-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6zgi format mmCIF fromDatabase pdb

Summary of feedback from opening 6zgi fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "NAG" near line 28731  
  
6zgi title:  
Furin Cleaved Spike Protein of SARS-CoV-2 in Closed Conformation [more
info...]  
  
Chain information for 6zgi #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6zgi #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
  

> set bgColor white

> select up

Nothing selected  

> select up

Nothing selected  

> name s1 :27-676

> name s2 :689-1147

> color s1 green

> color s2 red

> hide atoms

> show :614:854

> select :614:854

51 atoms, 45 bonds, 1 model selected  

> color byatom

> toolshed show Clashes

> toolshed show Contacts

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 0x12e31e090>  
  
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.  
  

> select :854

27 atoms, 24 bonds, 1 model selected  

> toolshed show Contacts

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 0x12df05c90>  
  
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.  
  

> select ~sel

26826 atoms, 27552 bonds, 12 pseudobonds, 2 models selected  

> select clear

> select /C:854

9 atoms, 8 bonds, 1 model selected  

> toolshed show Contacts

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 0x12e43de90>  
  
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.  
  

> set bgColor black

> toolshed show Contacts

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 0x12edca190>  
  
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 INTEL-14.7.8
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel 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 → Error saving settings

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Mika,

Thanks for reporting this problem. The code generating the error was changed back in March. Please try the 1.1 release instead of the 0.93 release you are currently using. If you still get an error, please submit another bug report.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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