Settings save failure when saving non-default color

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\lijin\\\Desktop\\\model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) rbbp7iso2 [more info...]  
  
Chain information for model.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in model.pdb #1  
---  
ARS — (ARS)  
  
Alignment identifier is 1.A  

> style sel stick

Changed 14 atom styles  

> hide sel cartoons

> show sel atoms

> color sel byhetero

> select sel :< 3

39 atoms, 39 bonds, 1 model selected  

> show sel atoms

> color sel byhetero

> hide sel cartoons

> toolshed show Rotamers

> swapaa interactive sel MET lib Dunbrack

/A TRP 401: phi -149.9, psi 155.9 trans  

> swapaa #1/A:401 MET criteria 1

Using Dunbrack library  
model.pdb #1/A TRP 401: phi -149.9, psi 155.9 trans  
Applying MET rotamer (chi angles: 63.7 -173.4 72.0) to model.pdb #1/A MET 401  

> swapaa interactive sel MET lib Dunbrack

/A MET 401: phi -149.9, psi 155.9 trans  

> swapaa #1/A:401 MET criteria 1 retain false

Using Dunbrack library  
model.pdb #1/A MET 401: phi -149.9, psi 155.9 trans  
Applying MET rotamer (chi angles: 63.7 -173.4 72.0) to model.pdb #1/A MET 401  

> toolshed show Clashes

> clashes select true

3 clashes  

> toolshed show Clashes

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\clashes\tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\clashes\gui.py", line 558, in get_command  
self.settings.save(settings=saveables)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\settings.py", line 205, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 359, in __setattr__  
self._session, value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 488, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 482, in convert_from_string  
return self.from_str(str_value)  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 46, in literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
[0. 1. 0.49803922 1. ]  
^  
SyntaxError: invalid syntax  
  
File "", line 1  
[0. 1. 0.49803922 1. ]  
^  
SyntaxError: invalid syntax  
  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  

> toolshed show Contacts

> toolshed show Clashes

> clashes select true

3 clashes  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\clashes\tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\clashes\gui.py", line 558, in get_command  
self.settings.save(settings=saveables)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\settings.py", line 205, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 359, in __setattr__  
self._session, value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 488, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 482, in convert_from_string  
return self.from_str(str_value)  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 46, in literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
[0.6666667 1. 0. 1. ]  
^  
SyntaxError: invalid syntax  
  
File "", line 1  
[0.6666667 1. 0. 1. ]  
^  
SyntaxError: invalid syntax  
  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\clashes\tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\clashes\gui.py", line 558, in get_command  
self.settings.save(settings=saveables)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\settings.py", line 205, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 359, in __setattr__  
self._session, value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 488, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\configfile.py", line 482, in convert_from_string  
return self.from_str(str_value)  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 46, in literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
[1. 0.33333334 0. 1. ]  
^  
SyntaxError: invalid syntax  
  
File "", line 1  
[1. 0.33333334 0. 1. ]  
^  
SyntaxError: invalid syntax  
  
File "C:\Program Files\ChimeraX\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13543 Core Profile Forward-Compatible Context 25.20.15002.58
OpenGL renderer: Radeon RX Vega M GH Graphics
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Happened because repr() of a Color was not eval()able (numpy string representation of the rgba).