Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5168 closed defect (fixed)

self._positions is None

Reported by: idocaspy@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.4.0-52-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd /scratch/EM_DATA/embl1120/MultiBody/job361/

Current working directory is: /scratch/EM_DATA/embl1120/MultiBody/job361  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> graphics silhouettes true

> lighting full

> lighting shadows false

> open analyse_component003_bin0??_zflip.mrc vseries true

Opened map series analyse_component003_bin001_zflip.mrc as #1, 10 images, grid
size 500,500,500, pixel 0.896, shown at level 0.00315, step 2, values float32  

> volume #1.* level 0.009 step 1

> surface dust #1.* size 8

> color #1.* medium spring green

> view matrix camera
> 0.22006,-0.0091867,-0.97544,-342.92,-0.97546,-0.0089471,-0.21998,97.888,-0.0067064,0.99992,-0.01093,246.96

> view matrix camera
> 0.22006,-0.0091867,-0.97544,-342.92,-0.97546,-0.0089471,-0.21998,97.888,-0.0067064,0.99992,-0.01093,246.96

> view matrix

camera position:
-0.21993,0.011935,-0.97544,-342.51,0.9755,-0.0032392,-0.21998,99.425,-0.005785,-0.99993,-0.01093,179.73  
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.5.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.6.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.7.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.8.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.9.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.10.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix camera
> -0.21993,0.011935,-0.97544,-342.51,0.9755,-0.0032392,-0.21998,99.425,-0.005785,-0.99993,-0.01093,179.73

> movie record

> vseries play #1 direction oscillate loop true maxFrameRate 12

> wait 100

> vseries stop #1

> movie encode /home/ido/Downloads/embl1120/PSII_stacked_movies/361_comp3.mp4
> framerate 10

Movie saved to /home/ido/.../PSII_stacked_movies/361_comp3.mp4  
  

> close session

> cd /scratch/EM_DATA/embl1120/MultiBody/job382/

Current working directory is: /scratch/EM_DATA/embl1120/MultiBody/job382  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> graphics silhouettes true

> lighting full

> lighting shadows false

> open analyse_component001_bin0??_zflip.mrc vseries true

Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Summary of feedback from opening files  
---  
notes | Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
7 messages similar to the above omitted  
  
Opened map series analyse_component001_bin001_zflip.mrc as #1, 10 images, grid
size 500,500,500, pixel 0.896, shown at level 0.00418, step 2, values float32  

> volume #1.* level 0.01 step 1

> surface dust #1.* size 8

> color #1.* magenta

> view matrix camera
> 0.14797,-0.9835,-0.10415,154.6,-0.98677,-0.13977,-0.08209,173.47,0.066173,0.11492,-0.99117,-452.94

> movie record

> vseries play #1 direction oscillate loop true maxFrameRate 12

> wait 100

> vseries stop #1

> movie encode /home/ido/Downloads/embl1120/PSII_stacked_movies/382_comp1.mp4
> framerate 10

Movie saved to /home/ido/.../PSII_stacked_movies/382_comp1.mp4  
  

> close session

> cd /scratch/EM_DATA/embl1120/MultiBody/job382/

Current working directory is: /scratch/EM_DATA/embl1120/MultiBody/job382  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> graphics silhouettes true

> lighting full

> lighting shadows false

> open analyse_component002_bin0??_zflip.mrc vseries true

Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Summary of feedback from opening files  
---  
notes | Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
Traceback (most recent call last):  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 91, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 162, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 201, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 275, in _get_info  
  
display = obj.display  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 365, in get_display  
  
return self._any_displayed_positions and len(self._positions) > 0  
  
TypeError: object of type 'NoneType' has no len()  
  
  
7 messages similar to the above omitted  
  
Opened map series analyse_component002_bin001_zflip.mrc as #1, 10 images, grid
size 500,500,500, pixel 0.896, shown at level 0.00421, step 2, values float32  

> volume #1.* level 0.01 step 1

> surface dust #1.* size 8

> color #1.* magenta

> view matrix camera
> -0.21993,0.011935,-0.97544,-342.51,0.9755,-0.0032392,-0.21998,99.425,-0.005785,-0.99993,-0.01093,179.73

> movie record

> vseries play #1 direction oscillate loop true maxFrameRate 12

> wait 100

> vseries stop #1

> movie encode /home/ido/Downloads/embl1120/PSII_stacked_movies/382_comp2.mp4
> framerate 10

Movie saved to /home/ido/.../PSII_stacked_movies/382_comp2.mp4  
  




OpenGL version: 3.3 (Core Profile) Mesa 20.0.8
OpenGL renderer: llvmpipe (LLVM 10.0.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: Gigabyte Technology Co., Ltd.
Model: X299 AORUS MASTER
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 20 Intel(R) Core(TM) i9-9820X CPU @ 3.30GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        9.8G         53G        390M         62G        114G
	Swap:          2.0G          0B        2.0G

Graphics:
	17:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1e04] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. Device [19da:2503]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Attachments (1)

test.zip (3.9 MB ) - added by Tom Goddard 4 years ago.
Example script producing the bug. Open test/test.cxc in ChimeraX 1.2.5 or daily build.

Change History (8)

comment:1 by Eric Pettersen, 4 years ago

Component: UnassignedGraphics
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionself._positions is None

comment:2 by Tom Goddard, 4 years ago

Looks like you opened a series of MRC maps, played through the series and recorded a movie. That all worked. Then you uses "close session" and tried the same process on another series of MRC maps and it gave an error. The error is because there is some closed model that is somehow still present and causing the errors. I will have to try this to see what is going wrong.

For now you can probably start a new ChimeraX for each volume series movie you make to avoid the problem. Sorry it does not work better. Hopefully I can fix it in the daily build today or this week.

comment:3 by Tom Goddard, 4 years ago

This is a bug in the Models panel. Somehow after the session is closed it still uses the closed models that it has cached. It only happens when your commands are run in a command script. Even then I only get it when I switch back and forth between running ChimeraX 1.2.5 and the ChimeraX daily -- apparently there is some race condition so running the same ChimeraX repeatedly does not give the error for me.

You can work around this bug by putting at the top of your command script "ui tool hide Models" to hide the Models panel.

I'll attach an example script that reproduces the product for Eric to fix it.

by Tom Goddard, 4 years ago

Attachment: test.zip added

Example script producing the bug. Open test/test.cxc in ChimeraX 1.2.5 or daily build.

comment:4 by Tom Goddard, 4 years ago

Cc: Tom Goddard added
Owner: changed from Tom Goddard to Eric Pettersen

Eric, Model panel is somehow caching the old models after "close session" and then throws errors trying to update itself with those old models. I've attached a test example.

comment:5 by Eric Pettersen, 4 years ago

Status: assignedaccepted

comment:6 by Eric Pettersen, 4 years ago

Resolution: fixed
Status: acceptedclosed

Okay, I've committed a "fix", but since I've never been able to actually reproduce the problem I would need someone else to test it.

in reply to:  8 comment:7 by goddard@…, 4 years ago

I tested my reproducible case with your fix and get no error.  Thanks.

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