Opened 4 years ago

Closed 4 years ago

Last modified 3 years ago

#6675 closed defect (can't reproduce)

Problem after 'close' without 'vseries stop'

Reported by: d.e.richman@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.13.0-39-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  

> ui tool show "Show Volume Menu"

> toolshed show

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA_J118/cryosparc_P5_J118_component_000/*.mrc
> vseries true

Opened map series J118_component_000_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.33, step 1, values float32  

> movieFramerate 10

Unknown command: movieFramerate 10  

> mseries movieFramerate 10

Missing or invalid "models" argument: invalid models specifier  

> mseries slider #1 movieFramerate 10

> mseries slider #1 movieFramerate 10 bounce

Expected a keyword  

> volume #1.1 level 0.1913

> coordset #1 bounce

Missing "bounce" keyword's argument  

> mseries slider #1 movieFramerate 10 bounce true

Expected a keyword  

> coordset #1 bounce true

No structures specified  

> coordset #1 1-20 bounce true

Expected a keyword  

> show #!1.1 models

> hide #!1.1 models

> hide #!1 models

> show #!1.1 models

> hide #!1.1 models

> hide #!1 models

> show #!1.2 models

> hide #!1.2 models

> hide #!1 models

> show #!1.1 models

> hide #!1 models

> view #1.1 clip false

No displayed objects specified.  

> show #!1.2 models

> show #!1.3 models

> hide #!1 models

> vseries play #1 direction oscillate

> vseries stop

Missing or invalid "series" argument: empty atom specifier  

> vseries stop #1

> show #!1 models

> vseries play #1 direction oscillate

> vseries stop #1

> vseries play #1 direction oscillate maxFrameRate 10

> vseries stop #1

> vseries play #1 direction oscillate maxFrameRate 16

> volume #1.9 level 0.1913 color #b2b2b2

> volume #1.9 level 0.114

> vseries stop #1

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA_J118/cryosparc_P5_J118_component_001/*.mrc
> vseries true

Opened map series J118_component_001_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.343, step 1, values float32  

> vseries play #1 direction oscillate maxFrameRate 16

> volume #1.1 level 0.3428 color #b2b2b2

> volume #1.1 level 0.08324

> vseries stop #1

> volume #1.11 level 0.272

> vseries play #1 direction oscillate maxFrameRate 16

> vseries stop #1

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA_J118/cryosparc_P5_J118_component_002/*.mrc
> vseries true

Opened map series J118_component_002_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.367, step 1, values float32  

> volume #1.1 level 0.2206

> vseries play #1 direction oscillate maxFrameRate 16

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_000/*.mrc
> vseries true

Opened map series J119_component_000_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.34, step 1, values float32  

> volume #1.1 level 0.2455

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_001/*.mrc
> vseries true

Opened map series J119_component_001_frame_000.mrc as #2, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.357, step 1, values float32  

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_001/*.mrc
> vseries true

Opened map series J119_component_001_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.357, step 1, values float32  

> volume #1.1 level 0.2311

> volume #1.1 level 0.2459

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J119_component_002/*.mrc
> vseries true

Opened map series J119_component_002_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.338, step 1, values float32  

> volume #1.1 level 0.2742

> volume #1.1 level 0.2467

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_000/*.mrc
> vseries true

Opened map series J120_component_000_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.349, step 1, values float32  

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> volume #1.15 level 0.309

> vseries play #1 direction oscillate maxFrameRate 8

> vseries stop #1

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_001/*.mrc
> vseries true

Opened map series J120_component_001_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.363, step 1, values float32  

> volume #1.1 level 0.3041

> vseries play #1 direction oscillate maxFrameRate 8

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_002/*.mrc
> vseries true

Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
  
return self._func(self._name, data)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py", line 275,
in _get_info  
  
display = obj.display  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
  
return self._func(self._name, data)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py", line 275,
in _get_info  
  
display = obj.display  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
  
return self._func(self._name, data)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py", line 275,
in _get_info  
  
display = obj.display  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
  
return self._func(self._name, data)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py", line 275,
in _get_info  
  
display = obj.display  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/core/triggerset.py", line 130,
in invoke  
  
return self._func(self._name, data)  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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 "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/model_panel/tool.py", line 275,
in _get_info  
  
display = obj.display  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c8/libexec/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()  
  
  
17 messages similar to the above omitted  
  
Opened map series J120_component_002_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.357, step 1, values float32  




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       6.1Gi        91Gi       301Mi        27Gi       118Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)	
	Subsystem: eVga.com. Corp. TU102 [GeForce RTX 2080 Ti] [3842:2281]	
	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-Clipper: 0.16.0
    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-ISOLDE: 1.2.2
    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

Change History (8)

comment:1 by pett, 4 years ago

Cc: pets added
Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem after 'close' without 'vseries stop'

Reported by Dan Richman

comment:2 by pett, 4 years ago

Cc: pett added; pets removed

comment:3 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Looks like you opened a volume series, played it, closed, and opened another series to produce this error. I tried the exact same steps in the current ChimeraX daily build and did not get any error. You are using ChimeraX 1.2.5 and you may want to update to ChimeraX 1.3 or a daily build.

My guess is that closing the volume series while it was playing had some bug in your old version of ChimeraX which may be fixed, or may only happen rarely.

open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_001/*.mrc
> vseries true

Opened map series J120_component_001_frame_000.mrc as #1, 20 images, grid size
120,120,120, pixel 2.12, shown at level 0.363, step 1, values float32  

> volume #1.1 level 0.3041

> vseries play #1 direction oscillate maxFrameRate 8

> close

> open
> /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_002/*.mrc
> vseries true

Error processing trigger "model display changed":  
TypeError: object of type 'NoneType' has no len()

in reply to:  4 ; comment:4 by d.e.richman@…, 3 years ago 

Interesting, thanks for checking. I use SBGrid and have had errors launching their 1.3 builds so I've stuck with 1.2.5, but I'll have to get back in touch with them.

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, April 21, 2022 8:10 PM
Cc: Dan Richman <d.e.richman@jhu.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6675: Problem after 'close' without 'vseries stop'


      External Email - Use Caution



#6675: Problem after 'close' without 'vseries stop'
--------------------------------------+-------------------------
          Reporter:  d.e.richman@…    |      Owner:  Tom Goddard
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Volume Data      |    Version:
        Resolution:  can't reproduce  |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => can't reproduce


Comment:

 Looks like you opened a volume series, played it, closed, and opened
 another series to produce this error.  I tried the exact same steps in the
 current ChimeraX daily build and did not get any error.  You are using
 ChimeraX 1.2.5 and you may want to update to ChimeraX 1.3 or a daily
 build.

 My guess is that closing the volume series while it was playing had some
 bug in your old version of ChimeraX which may be fixed, or may only happen
 rarely.

 {{{
 open
 >
 /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_001/*.mrc
 > vseries true

 Opened map series J120_component_001_frame_000.mrc as #1, 20 images, grid
 size
 120,120,120, pixel 2.12, shown at level 0.363, step 1, values float32

 > volume #1.1 level 0.3041

 > vseries play #1 direction oscillate maxFrameRate 8

 > close

 > open
 >
 /home/drichman/Downloads/cryosparc_P5_3DVA/cryosparc_P5_J120_component_002/*.mrc
 > vseries true

 Error processing trigger "model display changed":
 TypeError: object of type 'NoneType' has no len()
 }}}

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Ticket URL: <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F6675%23comment%3A3&amp;data=05%7C01%7Cd.e.richman%40jhu.edu%7C04a8a01342b2448532f408da23f47f7d%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637861830280702731%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=RJ1U25Ns42Y%2F%2B67lsPcKX43svIiyjpQXabe9gVvAwRk%3D&amp;reserved=0>
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in reply to:  5 ; comment:5 by goddard@…, 3 years ago 

Ok.  Let me know if SBGrid ChimeraX 1.3 is not working, give details how it fails, and I might be able to help.

in reply to:  6 ; comment:6 by d.e.richman@…, 3 years ago 

Hi Tom, pardon my delay. I included a bunch of information below about the errors if I install SBGrid's default ChimeraX (1.3).

Attempting to launch it the typical way in the sbgrid environment:

drichman@blackbird:~$ chimerax
The executable chimerax was not found.
The version of the application that contains chimerax may not be installed
or may not be configured in this shell.

Please check your version configuration in ~/.sbgrid.conf .

Email bugs@sbgrid.org for help or to report an error.

(There's no .sbgrid.conf)


The sbwhich command confirms it doesn't find the chimerax executable but does work otherwise, e.g.,

drichman@blackbird:~$ sbwhich chimerax
chimerax: Command not found.

drichman@blackbird:~$ sbwhich relion
/programs/x86_64-linux/relion/3.1.3_cu10.2/bin/relion


If I try its path directly, these are the errors:

drichman@blackbird:~$ /programs/x86_64-linux/chimerax/1.3/bin/chimerax
Traceback (most recent call last):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018, in <module>
    exit_code = init(sys.argv)
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 425, in init
    initialize_ssl_cert_dir()
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/utils.py", line 72, in initialize_ssl_cert_dir
    import ssl
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/ssl.py", line 98, in <module>
    import _ssl             # if we can't import it, let the error propagate
ImportError: libssl.so.10: cannot open shared object file: No such file or directory



Or the bin.capsules version:

drichman@blackbird:~$ /programs/x86_64-linux/chimerax/1.3/bin.capsules/chimerax
The executable chimerax was not found.

The version of the application that contains chimerax may not be installed
or may not be configured in this shell.
Please check your version configuration in ~/.sbgrid.conf .

Email bugs@sbgrid.org for help or to report an error.



If I instead install chimerax@1.2.5-c8, it does launch, just giving these warnings:

drichman@blackbird:~$ chimerax
WARNING: Release of profile requested but WebEnginePage still not deleted. Expect troubles !
WARNING: Release of profile requested but WebEnginePage still not deleted. Expect troubles !
WARNING: Release of profile requested but WebEnginePage still not deleted. Expect troubles !
________________________________
From: Tom Goddard <goddard@sonic.net>
Sent: Friday, April 22, 2022 3:46 PM
To: Dan Richman <d.e.richman@jhu.edu>
Cc: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6675: Problem after 'close' without 'vseries stop'


      External Email - Use Caution



Ok.  Let me know if SBGrid ChimeraX 1.3 is not working, give details how it fails, and I might be able to help.

On Apr 22, 2022, at 11:19 AM, Dan Richman <d.e.richman@jhu.edu<mailto:d.e.richman@jhu.edu>> wrote:

Interesting, thanks for checking. I use SBGrid and have had errors launching their 1.3 builds so I've stuck with 1.2.5, but I'll have to get back in touch with them.

comment:7 by Tom Goddard, 3 years ago

Thanks for the details about SBGrid ChimeraX 1.3 not working on Linux.

The fact that chimerax is not in the executable search path is an SBGrid installation problem, not something we control.

When you execute ChimeraX 1.3 with a full path it fails to start because it does not find the ssl (secure socket layer) networking library. I think that is because SBGrid is giving you the CentOS 7 version of ChimeraX and you are using Ubuntu 20.04 which has different system libraries (e.g. a different ssl library version). You could install ChimeraX for Ubuntu 20 from our web site and it would work. I don't know how or if SBGrid tries to handle different linux distributions. I will make a separate ChimeraX bug report and talk to SBGrid to see how they handle (or more likely don't handle) this.

in reply to:  8 ; comment:8 by d.e.richman@…, 3 years ago 

Thanks Tom, I'm curious to see what SBGrid says, thanks for pursuing this.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, May 5, 2022 3:41 PM
Cc: Dan Richman <d.e.richman@jhu.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6675: Problem after 'close' without 'vseries stop'


      External Email - Use Caution



#6675: Problem after 'close' without 'vseries stop'
--------------------------------------+-------------------------
          Reporter:  d.e.richman@…    |      Owner:  Tom Goddard
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Volume Data      |    Version:
        Resolution:  can't reproduce  |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+-------------------------

Comment (by Tom Goddard):

 Thanks for the details about SBGrid ChimeraX 1.3 not working on Linux.

 The fact that chimerax is not in the executable search path is an SBGrid
 installation problem, not something we control.

 When you execute ChimeraX 1.3 with a full path it fails to start because
 it does not find the ssl (secure socket layer) networking library.  I
 think that is because SBGrid is giving you the CentOS 7 version of
 ChimeraX and you are using Ubuntu 20.04 which has different system
 libraries (e.g. a different ssl library version).  You could install
 ChimeraX for Ubuntu 20 from our web site and it would work.  I don't know
 how or if SBGrid tries to handle different linux distributions.  I will
 make a separate ChimeraX bug report and talk to SBGrid to see how they
 handle (or more likely don't handle) this.

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