Opened 5 years ago

Closed 5 years ago

#3359 closed defect (fixed)

map/surface color is None

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005292300 (2020-05-29 23:00:06 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005292300 (2020-05-29)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/rodolphejazzar/Dropbox/Jesse_Folder/Cluster/WFN/Cu/WFN/MeTrisCuM06DEF2TZVPP_wfn.pdb
> format pdb

Summary of feedback from opening
/Users/rodolphejazzar/Dropbox/Jesse_Folder/Cluster/WFN/Cu/WFN/MeTrisCuM06DEF2TZVPP_wfn.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Generated by Multiwfn, Totally 84 atoms  
  
Ignored bad PDB record found on line 86  
END  
  

> open /Users/rodolphejazzar/Dropbox/Jesse_Folder/Cluster/WFN/Cu/WFN/ELF.cub
> format cube

Opened ELF.cub, grid size 141,137,92, pixel 0.139, shown at level
-0.974,0.974, step 1, values float32  

> volume #2 level -0.9735 level 0.2411

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 region 0,0,46,140,136,46

> volume #2 region 0,0,46,140,136,46

> style ball

Changed 84 atom styles  

> lighting flat

> lighting full

> show #2.2 models

> hide #2.2 models

> show #2.1 models

> hide #2.1 models

> hide #2.1 target m

> close #2.1

> show #2.2 models

> hide #2.2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2126, in mousePressEvent  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 365, in select_marker_cb  
cb(self.markers[i])  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2195, in selected_marker_cb  
self.select_data_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  

[_many_ of these tracebacks deleted]

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2126, in mousePressEvent  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 365, in select_marker_cb  
cb(self.markers[i])  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2195, in selected_marker_cb  
self.select_data_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2128, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2135, in mouseReleaseEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2132, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/histogram.py", line 414, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2203, in moved_marker_cb  
self.select_data_cb() # Causes redisplay using GUI settings  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2189, in select_data_cb  
d.redisplay_needed_cb()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 294, in redisplay_needed_cb  
self.redisplay_needed()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 320, in redisplay_needed  
self.show_using_dialog_settings(self.active_volume)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 360, in
show_using_dialog_settings  
p.use_gui_settings(dr)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1666, in use_gui_settings  
hp.set_threshold_parameters_from_gui()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2765, in
set_threshold_parameters_from_gui  
if tuple(s.rgba) != tuple(color):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1967, in _get_rgba  
return tuple(c/255 for c in self.color)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1995, in get_color  
return Surface.get_color(self)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  

> show #2.3 target m

> view #2.3 clip false

No displayed objects specified.  

> transparency #1#2.3#!2 50

> vop gaussian #2 sdev 0.416

> volume #3 level -2.047e-16,0 level 0.6713,0.8 level 0.8648,1

> volume #3 level -2.047e-16,0 level 0.8079,0.5147 level 0.8648,1

> close #3

> show #2.2 models

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 region 0,0,45,140,136,45

> volume #2 region 0,0,45,140,136,45

> volume #2 level 0,1 level 0,0.8 level 0,0 level 0,0 level 0.9884,0.8 level
> 0.9998,1

> volume #2 level 0,1 level 0,0.8 level 0,0 level 0,0 level 0.9848,1 level
> 0.9998,1

> volume #2 level 0,1 level 0,0.8 level 0,0 level 0,0.04412 level 0.9848,1
> level 0.9998,1

> volume #2 step 2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3947, in _update_drawings  
v.update_drawings()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 754, in update_drawings  
self._keep_displayed_data = self.displayed_matrices()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1696, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1185, in matrix  
m = self.region_matrix(r, read_matrix)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1209, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/gaussian/gaussian_grid.py", line 42, in read_matrix  
matrix = self.gc.matrix(self.component_number, progress)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/gaussian/gaussian_format.py", line 120, in matrix  
if self.matrices == None:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "graphics update":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/gaussian/gaussian_format.py", line 120, in matrix  
if self.matrices == None:  
  
See log for complete Python traceback.  
  

> volume #2 step 1

> volume #2 level 0,1 level 0,0.8 level 0,0 level 1,0.04412 level 0.9848,1
> level 0.9998,1

> volume #2 region 0,0,0,140,136,91 step 8

> volume #2 style surface region 0,0,0,140,136,91 step 8

> volume #2 style mesh

> volume #2 style surface style image maximumIntensityProjection True

Repeated keyword argument "style"  

> volume #2 region 0,0,40,140,136,40 step 1 maximumIntensityProjection false
> showOutlineBox true

> volume #2 step 4

> volume #2 step 1

> volume #2 level 0,1 level 0,0.8 level 0,0 level 0,0.04412 level 0.9848,1
> level 0.9998,1

> hide #2.3 models

> show #2.3 models




OpenGL version: 4.1 INTEL-12.10.17
OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro9,2
      Processor Name: Intel Core i7
      Processor Speed: 2.9 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 231.0.0.0.0
      SMC Version (system): 2.2f44
      Sudden Motion Sensor:
          State: Enabled

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G4032)
      Kernel Version: Darwin 18.7.0
      Time since boot: 13 days 23:40

Graphics/Displays:

    Intel HD Graphics 4000:

      Chipset Model: Intel HD Graphics 4000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0166
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1280 x 800
          UI Looks like: 1280 x 800
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (4)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → map/surface color is None

comment:2 by Tom Goddard, 5 years ago

There is a second error in the log about gaussian_format.py.

comment:3 by Tom Goddard, 5 years ago

First bug is closing surface submodel of volume probably with Model Panel or "close #1.1" does it, then using Volume Viewer to change the threshold level on the histogram which apparently does not realize the surface is gone.

comment:4 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made volume viewer handle situation where surface is closed. Already handled image submodel being closed.
Also fixed gaussian format reader testing numpy array == None instead of is None, and fixed a few other places that could happen.

Note: See TracTickets for help on using tickets.