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.