Opened 7 years ago

Closed 7 years ago

#1795 closed defect (duplicate)

self._positions is None

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

Description 

The following bug report has been submitted:
Platform:        Darwin-16.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-02)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-03-02)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Julia/Desktop/ETH/Kaspar/hOST/chimerax/session-5.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/preset_mgr/manager.py", line 48, in restore_snapshot  
return session.preset_mgr  
AttributeError: 'Session' object has no attribute 'preset_mgr'  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3482, in _update_drawings  
if v.display:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "graphics update": object of type 'NoneType' has no
len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  

> open /Users/Julia/Desktop/ETH/Kaspar/hOST/chimerax/session-3.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/preset_mgr/manager.py", line 48, in restore_snapshot  
return session.preset_mgr  
AttributeError: 'Session' object has no attribute 'preset_mgr'  
  
opened ChimeraX session  

> open /Users/Julia/Desktop/ETH/Kaspar/hOST/hOSTA-Relion/session-chimerax2.cxs

opened ChimeraX session  

> ui mousemode rightMode select

Opened relion-postprocess-hOSTfull-job090-371A-resampled-on-mapA1.mrc, grid
size 384,384,384, pixel 0.84, shown at level 0.00585, step 2, values float32  
Summary of feedback from opening
/Users/Julia/Desktop/ETH/Kaspar/hOST/chimerax/hOSTB_190228_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 43  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 44  
BOND : 0.006 0.086 18307  
  
Ignored bad PDB record found on line 45  
ANGLE : 0.985 13.849 24945  
  
Ignored bad PDB record found on line 46  
CHIRALITY : 0.059 0.337 2889  
  
Ignored bad PDB record found on line 47  
PLANARITY : 0.008 0.068 2987  
  
15 messages similar to the above omitted  
  
Chain information for hOSTB_190228_refined.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
  
Opened relion-hOSTB-full-nobelt-postprocess-job256-354A-aligned.mrc, grid size
384,384,384, pixel 0.84, shown at level 0.00601, step 2, values float32  
Summary of feedback from opening
/Users/Julia/Desktop/ETH/Kaspar/hOST/chimerax/hOSTA_real_space_refined_61.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.006 0.081 17576  
  
Ignored bad PDB record found on line 23  
ANGLE : 1.016 15.992 23924  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.060 0.379 2801  
  
17 messages similar to the above omitted  
  
Chain information for hOSTA_real_space_refined_61.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> hide #!1 models

> hide #!3 models

> hide #!1.1 models

> show #!1.1 models

> hide #!6 models

> hide #!6.1 models

> hide #!5.1 models

> hide #!5 models

> hide #!3.1 models

> hide #!4 models

> show #!4 models

> hide #!4.1 models

> hide #!1.1 models

> hide #!1 models

> show #!1 models

> toolshed show '"Density Map Toolbar"'

> toolshed show Toolbar

> toolshed show '"Basic Actions"'

> show #!2 models

> hide #!2 models

> hide #!4 models

> color zone #2 near #1 distance 10

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!5 models

> show #!5 models

> show selAtoms

> show selAtoms ribbons

> show selAtoms surfaces

> volume selMaps style surface

> volume selMaps style surface

> select #1

3 models selected  

> select #2

16558 atoms, 16971 bonds, 10 pseudobonds, 1 model selected  

> show #!2 models

> show #!1.1 models

> hide #!1.1 models

> hide #!1 models

> hide #!2 models

> show #!1.1 models

> volume selMaps show

> volume selMaps show

> volume selMaps show

> volume selMaps show

> volume selMaps show

> show #!2 models

> show #!3.1 models

> show #!4 models

> show #!4.1 models

> show #!5.1 models

> show #!6 models

> hide #!6 models

> close #6

> close #2

> close

> open /Users/Julia/Desktop/ETH/Kaspar/hOST/chimerax/relion-postprocess-
hOSTfull-job090-371A-resampled-on-mapA1.mrc

Opened relion-postprocess-hOSTfull-job090-371A-resampled-on-mapA1.mrc, grid
size 384,384,384, pixel 0.84, shown at level 0.00585, step 2, values float32  

> close

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4872, in models_opened  
cb(vlist)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 188, in volume_opened_cb  
self.display_volume_info(v)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 233, in display_volume_info  
p.update_panel_widgets(volume)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1635, in update_panel_widgets  
self.add_histogram_pane(volume)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 1519, in add_histogram_pane  
hp.set_data_region(v)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2121, in set_data_region  
self.update_threshold_gui()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2538, in update_threshold_gui  
self.update_shown_icon()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 2329, in update_shown_icon  
shown = v.display  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "add models": object of type 'NoneType' has no len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.25.19
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by pett, 7 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → self._positions is None

comment:2 by pett, 7 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed last month.

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