Opened 6 years ago

Closed 6 years ago

#2891 closed defect (duplicate)

Sequence viewer: 'OptionalRGBAOption' object has no attribute 'get'

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
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: 0.91 (2019-06-08)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-06-08)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> save /Users/chin25/Desktop/image2.png supersample 3

> open /Users/chin25/Desktop/EM/2a-rigor/sharpened_map.ccp4

Opened sharpened_map.ccp4, grid size 512,512,512, pixel 1.08, shown at level
2.93, step 2, values float32  

> close

> open /Users/chin25/Desktop/EM/2a-rigor/rigor-sharpsharpened_map.ccp4

Opened rigor-sharpsharpened_map.ccp4, grid size 520,520,520, pixel 1.08, shown
at level 4.5, step 4, values float32  

> open
/Users/chin25/Desktop/EM/2a-rigor/RealSpaceRefine_28/a_real_space_refined-
coot-11.pdb

Chain information for a_real_space_refined-coot-11.pdb #2  
---  
Chain | Description  
A C D E | No description available  
B | No description available  
F | No description available  
G I | No description available  
H | No description available  
  

> volume zone #1 nearAtoms #2 range 3

> style selAtoms stick

Changed 29327 atom styles  

> set bgColor white

> rainbow selAtoms

> rainbow selAtoms

> hide selAtoms

> show selAtoms ribbons

> show selAtoms ribbons

> hide selAtoms surfaces

> hide selAtoms ribbons

> open /Users/chin25/Desktop/EM/2a-adp/refine3D/run_class001.mrc

Opened run_class001.mrc, grid size 520,520,520, pixel 1.08, shown at level
0.00801, step 4, values float32  

> volume zone #4 nearAtoms #2 range 3

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #2

> open /Users/chin25/Desktop/EM/2a-adp/RealSpaceRefine_6/last_frame_rsr-
coot-6_real_space_refined.pdb

Chain information for last_frame_rsr-coot-6_real_space_refined.pdb #1  
---  
Chain | Description  
A | No description available  
B C E F G | No description available  
D | No description available  
  

> open /Users/chin25/Desktop/EM/2a-adp/potprocess/sharpened_map.ccp4

Opened sharpened_map.ccp4, grid size 520,520,520, pixel 1.06, shown at level
4.52, step 4, values float32  

> fitmap #4 inMap #2

Fit map run_class001.mrc in map sharpened_map.ccp4 using 1406729 points  
correlation = 0.9237, correlation about mean = 0.5938, overlap = 9.619e+04  
steps = 80, shift = 9.31, angle = 0.236 degrees  
  
Position of run_class001.mrc (#4) relative to sharpened_map.ccp4 (#2)
coordinates:  
Matrix rotation and translation  
0.99999153 0.00411631 -0.00000364 -6.35914298  
-0.00411631 0.99999153 -0.00002034 -4.03590644  
0.00000356 0.00002035 1.00000000 -5.70808913  
Axis 0.00494257 -0.00087509 -0.99998740  
Axis point -982.44823098 1549.66185988 0.00000000  
Rotation angle (degrees) 0.23585103  
Shift along axis 5.68011852  
  

> show selAtoms ribbons

> style selAtoms stick

Changed 22003 atom styles  

> show selAtoms ribbons

> hide selAtoms

> volume zone #4 nearAtoms #1 range 3

> volume zone #2 nearAtoms #1 range 3

> lighting soft

> volume selMaps step 2

> volume selMaps step 1

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

Unknown command: elect :.B:.C:.E:.F:.G  

Expected an objects specifier or a keyword  

> toolshed show Registration

Please register the custom scheme 'cxreg' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
chinthalapudi.1@osu.edu is subscribed to the ChimeraX announcements list  
Alignment identifier is 1.A  
Alignment identifier is 1  
Alignment identifier is 1.D  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select /A

6404 atoms, 6527 bonds, 1 pseudobond, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 482, in <lambda>  
mcb.color_changed.connect(lambda c, s=self: s.make_callback())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 170, in make_callback  
self._callback(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 41, in <lambda>  
self._setting_change_cb(cat, o), attr_name=attr_name, settings=sv.settings,
**ctor_keywords)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
  
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/ui/options/options.py", line 482, in <lambda>  
mcb.color_changed.connect(lambda c, s=self: s.make_callback())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 170, in make_callback  
self._callback(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 41, in <lambda>  
self._setting_change_cb(cat, o), attr_name=attr_name, settings=sv.settings,
**ctor_keywords)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
  
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/ui/options/options.py", line 478, in <lambda>  
cb.clicked.connect(lambda state, s=self: s.make_callback())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 170, in make_callback  
self._callback(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 41, in <lambda>  
self._setting_change_cb(cat, o), attr_name=attr_name, settings=sv.settings,
**ctor_keywords)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
  
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/ui/options/options.py", line 478, in <lambda>  
cb.clicked.connect(lambda state, s=self: s.make_callback())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 170, in make_callback  
self._callback(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 41, in <lambda>  
self._setting_change_cb(cat, o), attr_name=attr_name, settings=sv.settings,
**ctor_keywords)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
  
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/ui/options/options.py", line 478, in <lambda>  
cb.clicked.connect(lambda state, s=self: s.make_callback())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 170, in make_callback  
self._callback(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 41, in <lambda>  
self._setting_change_cb(cat, o), attr_name=attr_name, settings=sv.settings,
**ctor_keywords)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
AttributeError: 'OptionalRGBAOption' object has no attribute 'get'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/settings_tool.py", line 87, in _setting_change_cb  
colors = [opt.get(), None]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro Vega 64 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (4)

comment:1 by Eric Pettersen, 6 years ago

Platform: all
Project: ChimeraX
Resolution: duplicate
Status: newclosed

comment:2 by Eric Pettersen, 6 years ago

Component: UnassignedSequence
Resolution: duplicate
Status: closedreopened
Summary: ChimeraX bug report submissionSequence viewer: 'OptionalRGBAOption' object has no attribute 'get'

comment:3 by Eric Pettersen, 6 years ago

Owner: set to Eric Pettersen
Status: reopenedaccepted

comment:4 by Eric Pettersen, 6 years ago

Resolution: duplicate
Status: acceptedclosed
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