Opened 2 years ago

Closed 2 years ago

#9224 closed defect (can't reproduce)

Crash showing vseries

Reported by: sudipag@… 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:        Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed
During Vseries display 
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

> ui tool show "Volume Viewer"

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_000.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_001.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_002.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_003.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_004.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_005.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_006.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_007.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_008.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_009.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_010.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_011.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_012.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_013.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_014.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_015.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_016.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_017.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_018.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_019.mrc"

Opened J499_component_000_frame_000.mrc as #1.1, grid size 400,400,400, pixel
0.813, shown at level 0.0193, step 2, values float32  
Opened J499_component_000_frame_001.mrc as #1.2, grid size 400,400,400, pixel
0.813, shown at level 0.0193, step 2, values float32  
Opened J499_component_000_frame_002.mrc as #1.3, grid size 400,400,400, pixel
0.813, shown at level 0.0193, step 2, values float32  
Opened J499_component_000_frame_003.mrc as #1.4, grid size 400,400,400, pixel
0.813, shown at level 0.0193, step 2, values float32  
Opened J499_component_000_frame_004.mrc as #1.5, grid size 400,400,400, pixel
0.813, shown at level 0.0194, step 2, values float32  
Opened J499_component_000_frame_005.mrc as #1.6, grid size 400,400,400, pixel
0.813, shown at level 0.0194, step 2, values float32  
Opened J499_component_000_frame_006.mrc as #1.7, grid size 400,400,400, pixel
0.813, shown at level 0.0194, step 2, values float32  
Opened J499_component_000_frame_007.mrc as #1.8, grid size 400,400,400, pixel
0.813, shown at level 0.0195, step 2, values float32  
Opened J499_component_000_frame_008.mrc as #1.9, grid size 400,400,400, pixel
0.813, shown at level 0.0196, step 2, values float32  
Opened J499_component_000_frame_009.mrc as #1.10, grid size 400,400,400, pixel
0.813, shown at level 0.0197, step 2, values float32  
Opened J499_component_000_frame_010.mrc as #1.11, grid size 400,400,400, pixel
0.813, shown at level 0.0197, step 2, values float32  
Opened J499_component_000_frame_011.mrc as #1.12, grid size 400,400,400, pixel
0.813, shown at level 0.0197, step 2, values float32  
Opened J499_component_000_frame_012.mrc as #1.13, grid size 400,400,400, pixel
0.813, shown at level 0.0198, step 2, values float32  
Opened J499_component_000_frame_013.mrc as #1.14, grid size 400,400,400, pixel
0.813, shown at level 0.0198, step 2, values float32  
Opened J499_component_000_frame_014.mrc as #1.15, grid size 400,400,400, pixel
0.813, shown at level 0.0198, step 2, values float32  
Opened J499_component_000_frame_015.mrc as #1.16, grid size 400,400,400, pixel
0.813, shown at level 0.0198, step 2, values float32  
Opened J499_component_000_frame_016.mrc as #1.17, grid size 400,400,400, pixel
0.813, shown at level 0.0199, step 2, values float32  
Opened J499_component_000_frame_017.mrc as #1.18, grid size 400,400,400, pixel
0.813, shown at level 0.0199, step 2, values float32  
Opened J499_component_000_frame_018.mrc as #1.19, grid size 400,400,400, pixel
0.813, shown at level 0.02, step 2, values float32  
Opened J499_component_000_frame_019.mrc as #1.20, grid size 400,400,400, pixel
0.813, shown at level 0.02, step 2, values float32  

>

Incomplete command: vseries  

> play

Unknown command: play  

> select #1

41 models selected  

> play

Unknown command: play  

> ui tool show "Show Volume Menu"

> volume #1.12 color red

>

Incomplete command: vseries  

> view

> view orient

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting simple

> ui tool show Toolbar

> oscillate

Unknown command: oscillate  

> oscillate 1.1 1.2 1.3

Unknown command: oscillate 1.1 1.2 1.3  

> help help:user/tools/modelpanel.html

> volume all hide

> movie record

> vop morph #0 playStep 0.05 frames 20

volume morph requires 2 or more volumes, got 0  

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show #!1.1 models

> show #!1.3 models

> hide #!1.3 models

> hide #!1.1 models

> hide #!1.2 models

> show #!1.1 models

> show #!1.2 models

> show #!1.3 models

> show #!1.4 models

> show #!1.5 models

> show #!1.7 models

> show #!1.6 models

> show #!1.8 models

> show #!1.9 models

> show #!1.10 models

> show #!1.11 models

> show #!1.12 models

> show #!1.13 models

> show #!1.14 models

> show #!1.15 models

> show #!1.16 models

> show #!1.17 models

> show #!1.18 models

> show #!1.19 models

> show #!1.20 models

> ui tool show "Volume Viewer"

> open "Y:\sudipag\Sudipa\Projects\2023\CRBN-DDB1-HPK1\Reanalysis of older
> datasets in cryosparc\Maps for Chimera\cryosparc_P39_J458_component_0.mrc"
> format mrc

Opened cryosparc_P39_J458_component_0.mrc as #2, grid size 400,400,400, pixel
0.813, shown at level 8.17e-05, step 2, values float32  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> color #2 #ffff7f models transparency 0

> open "Y:\sudipag\Sudipa\Projects\2023\CRBN-DDB1-HPK1\Reanalysis of older
> datasets in cryosparc\Maps for Chimera\cryosparc_P39_J458_component_1.mrc"
> format mrc

Opened cryosparc_P39_J458_component_1.mrc as #3, grid size 400,400,400, pixel
0.813, shown at level 0.000156, step 2, values float32  

> open "Y:\sudipag\Sudipa\Projects\2023\CRBN-DDB1-HPK1\Reanalysis of older
> datasets in cryosparc\Maps for Chimera\cryosparc_P39_J458_component_2.mrc"
> format mrc

Opened cryosparc_P39_J458_component_2.mrc as #4, grid size 400,400,400, pixel
0.813, shown at level 0.00013, step 2, values float32  

> color #3 #ffaaff models transparency 0

> hide #!1 models

> select #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,68.857,0,1,0,161.2,0,0,1,40.64

> view matrix models #2,1,0,0,69.163,0,1,0,161.89,0,0,1,37.047

> ~select #2

Nothing selected  

> select #4

2 models selected  

> select #2

2 models selected  

> view matrix models #2,1,0,0,-63.079,0,1,0,-147.63,0,0,1,-30.501

> ~select #2

Nothing selected  

> ~select #4

Nothing selected  

> select #4

2 models selected  

> view matrix models #4,1,0,0,59.359,0,1,0,138.94,0,0,1,30.857

> set bgColor white

> volume #1.1 step 1

> volume #1.2 step 1

> volume #2 step 1

> volume #3 step 1

> volume #4 step 1

> volume #2 level 0.00013

> volume #3 level 0.00013

> ~select #4

Nothing selected  

> hide #!2 models

> hide #2.1 models

> hide #!3 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models

> vseries play #1 loop true

No volume series specified  

> select #1

41 models selected  

> vseries play #1 loop true

No volume series specified  

> vseries play #1 loop true

No volume series specified  

> ~select #1

Nothing selected  

> ~select #1.1

Nothing selected  

> ~select #1.2

Nothing selected  

> ~select #1.3

Nothing selected  

> ~select #1.4

Nothing selected  

> ~select #1.5

Nothing selected  

> ~select #1.6

Nothing selected  

> ~select #1.7

Nothing selected  

> ~select #1.8

Nothing selected  

> ~select #1.9

Nothing selected  

> ~select #1.10

Nothing selected  

> ~select #1.11

Nothing selected  

> ~select #1.12

Nothing selected  

> ~select #1.13

Nothing selected  

> ~select #1.14

Nothing selected  

> ~select #1.15

Nothing selected  

> ~select #1.16

Nothing selected  

> ~select #1.17

Nothing selected  

> ~select #1.18

Nothing selected  

> ~select #1.19

Nothing selected  

> ~select #1.20

Nothing selected  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.20 models

> hide #!1.19 models

> hide #!1.18 models

> hide #!1.17 models

> hide #!1.16 models

> hide #!1.15 models

> hide #!1.14 models

> hide #!1.13 models

> hide #!1.12 models

> hide #!1.11 models

> hide #!1.10 models

> hide #!1.9 models

> hide #!1.8 models

> hide #!1.7 models

> hide #!1.6 models

> hide #!1.5 models

> hide #!1.4 models

> hide #!1.3 models

> hide #!1.2 models

> hide #!1.1 models

> show #!1.1 models

> show #!1.4 models

> show #!1.5 models

> hide #!1.5 models

> show #!1.7 models

> vseries play #1.1 1.4 1.7 loop true

Expected a keyword  

> vseries play #1 loop 1.1 1.4 1.7

Invalid "loop" argument: Expected true or false (or 1 or 0)  

> vseries play #1 loop true

No volume series specified  

> show #!1.2 models

> show #!1.3 models

> show #!1.5 models

> show #!1.6 models

> show #!1.8 models

> show #!1.9 models

> show #!1.11 models

> show #!1.10 models

> show #!1.12 models

> show #!1.13 models

> show #!1.14 models

> show #!1.15 models

> show #!1.16 models

> show #!1.17 models

> show #!1.18 models

> show #!1.19 models

> show #!1.20 models

> vseries play #1 loop true

No volume series specified  

> hide #!1 models

> hide #!1.1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!2 models

> show #!2 models

> select #2

2 models selected  

> show #!1.1 models

> hide #!1 models

> color #2 #ffaa00 models transparency 0

> ~select #2

Nothing selected  

> color #2 yellow models transparency 0

> show #!2 target m

> select #2

2 models selected  

> show #!2 target m

> ~select #2

Nothing selected  

> select #2

2 models selected  

> ~select #2

Nothing selected  

> hide #!3 models

> show #!3 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\movie\movie.py", line 172, in capture_image  
i.save(save_path, self.img_fmt)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\PIL\Image.py", line
2235, in save  
save_handler(self, fp, filename)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\PIL\PpmImagePlugin.py", line 149, in _save  
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\PIL\ImageFile.py",
line 536, in _save  
s = e.encode_to_file(fh, bufsize)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "frame drawn":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\PIL\ImageFile.py",
line 536, in _save  
s = e.encode_to_file(fh, bufsize)  
  
See log for complete Python traceback.  
  

> show #!2 target m

> hide #!3 models

> hide #!4 models

> hide #!2 models

> show #!1 models

> show #!3 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> hide #!3 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> open vseries true

'vseries' has no suffix  

> open vseries #1 true

'vseries' has no suffix  

> open vseries #1 true

'vseries' has no suffix  

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_000.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_001.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_002.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_003.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_004.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_005.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_006.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_007.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_008.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_009.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_010.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_011.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_012.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_013.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_014.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_015.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_016.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_017.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_018.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_000/J499_component_000_frame_019.mrc"
> vseries true

Opened map series J499_component_000_frame_000.mrc as #5, 20 images, grid size
400,400,400, pixel 0.813, shown at level 0.0193, step 2, values float32  

> close #1

> play#5 loop true

Unknown command: vseries play#5 loop true  

> show #5.2 models

> show #5.3 models

> hide #5.3 models

> show #5.3 models

> hide #!5.3 models

> show #!5.3 models

> show #5.4 models

> hide #!5.4 models

> show #!5.4 models

> show #5.5 models

> show #5.6 models

> show #5.7 models

> hide #!5.7 models

> show #!5.7 models

> show #5.8 models

> show #5.9 models

> show #5.10 models

> show #5.11 models

> show #5.12 models

> show #5.13 models

> show #5.14 models

> show #5.15 models

> show #5.16 models

> show #5.18 models

> show #5.17 models

> show #5.19 models

> show #5.20 models

> play#5 loop true

Unknown command: vseries play#5 loop true  

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_000.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_001.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_002.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_003.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_004.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_005.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_006.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_007.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_008.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_009.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_010.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_011.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_012.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_013.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_014.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_015.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_016.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_017.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_018.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_001/J499_component_001_frame_019.mrc"
> vseries true

Opened map series J499_component_001_frame_000.mrc as #1, 20 images, grid size
400,400,400, pixel 0.813, shown at level 0.0179, step 2, values float32  

> play#1 loop true

Unknown command: vseries play#1 loop true  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!5 models

> show #!1 models

> volume #5.1 level 0.03689

> play#1 loop true

Unknown command: vseries play#1 loop true  

> play#1 loop

Unknown command: vseries play#1 loop  

> play#5 loop

Unknown command: vseries play#5 loop  

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!1 models

> show #!5 models

> play#5 loop

Unknown command: vseries play#5 loop  

> hide #!5 models

> show #!1 models

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_000.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_001.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_002.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_003.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_004.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_005.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_006.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_007.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_008.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_009.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_010.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_011.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_012.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_013.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_014.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_015.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_016.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_017.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_018.mrc"
> "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older datasets
> in cryosparc/3D variability
> display/cryosparc_P39_J499_component_002/J499_component_002_frame_019.mrc"
> vseries true

Opened map series J499_component_002_frame_000.mrc as #6, 20 images, grid size
400,400,400, pixel 0.813, shown at level 0.0185, step 2, values float32  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!6 models

> show #!2 models

> show #!6 models

> show #!5 models

> show #!1 models

> hide #!1 models

> hide #!6 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> show #!6 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> hide #!1 models

> show #!6 models

> hide #!6 models

> show #!1 models

> volume #6.1 level 0.03336

> hide #!1 models

> show #!1 models

> show #!2 models

> select #2

2 models selected  

> show #2.1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> ~select #2.1

1 model selected  

> ~select #2

Nothing selected  

> hide #!1 models

> show #!3 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> play#1 loop true

Unknown command: vseries play#1 loop true  

> vseries play #1 loop true

> volume #5.1 step 1

QFileSystemWatcher::addPaths: list is empty  

> save "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/3D variability display/Component1/movie_session.cxs"
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 203, in allocate_array  
m = alloc(shape, value_type)  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an
array with shape (400, 400, 400) and data type float32  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data  
s['array'] = dt.matrix().tobytes()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_grid.py", line 44, in read_matrix  
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_format.py", line 284, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 27, in read_array  
m = read_full_array(path, byte_offset, full_size,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 72, in read_full_array  
a = allocate_array(size, type)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 208, in allocate_array  
report_memory_error(msize, value_type, progress)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 229, in report_memory_error  
raise UserError(e)  
chimerax.core.errors.UserError: Could not allocate 244 Mbyte array of size
400,400,400 and type float32.  
  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
 ->
 'surface' ->

'J499_component_000_frame_009.mrc' ->   
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' ->  ->  'surface' ->  'J499_component_000_frame_009.mrc' ->
: Error while
saving session data for 'models' ->  ->  'surface' ->  'J499_component_000_frame_009.mrc' ->
  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J499_component_000_frame_009.mrc' -> : Error while saving session data for
'models' -> -> 'surface' -> 'J499_component_000_frame_009.mrc' ->  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 203, in allocate_array  
m = alloc(shape, value_type)  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an
array with shape (400, 400, 400) and data type float32  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data  
s['array'] = dt.matrix().tobytes()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_grid.py", line 44, in read_matrix  
return self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\mrc\mrc_format.py", line 284, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 27, in read_array  
m = read_full_array(path, byte_offset, full_size,  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 72, in read_full_array  
a = allocate_array(size, type)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 208, in allocate_array  
report_memory_error(msize, value_type, progress)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 229, in report_memory_error  
raise UserError(e)  
chimerax.core.errors.UserError: Could not allocate 244 Mbyte array of size
400,400,400 and type float32.  
  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
 ->
 'surface' ->

'J499_component_000_frame_009.mrc' ->   
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in   
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' ->  ->  'surface' ->  'J499_component_000_frame_009.mrc' ->
: Error while
saving session data for 'models' ->  ->  'surface' ->  'J499_component_000_frame_009.mrc' ->
  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J499_component_000_frame_009.mrc' -> : Error while saving session data for
'models' -> -> 'surface' -> 'J499_component_000_frame_009.mrc' ->  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> vseries save #1 ~/Desktop/test.cmap subregion 100,0,0,200,511,150 threshold
> 140 valueType uint8

> vseries play #5 loop true

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> save "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/3D variability display/Component0/movie.cxs"

> movie record

Already recording a movie  

> volume all hide

> movie record

Already recording a movie  

> volume all hide

> movie record

Already recording a movie  

> volume all hide

> movie record

Already recording a movie  

> volume all hide

> movie record

Already recording a movie  

> volume all hide

> movie record

Already recording a movie  

> vseries play #6 loop true

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!5 models

> show #!1 models

> color #5 #ffaaff models transparency 0

> color #5 #55ff00 models transparency 0

> color #5 cyan models transparency 0

> hide #!1 models

> hide #!5 models

> hide #!6 models

> show #!1 models

Error processing trigger "graphics update":  
  
You deleted or moved a volume file that is still open in ChimeraX.  
  
None  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.9168
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20XXS0KR00
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,868,499,456
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 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 → Crash showing vseries

Reported by Sudipa Rijal

comment:2 by Tom Goddard, 2 years ago

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

I don't see any clues in this bug report about why ChimeraX crashed showing a volume series.

I do see many error messages

"OSError: [Errno 28] No space left on device"

which means you have no disk space left. That could possibly be related to the crash. A more common cause of crashes is graphics driver bugs. You graphics driver is from 2021 and updating it may help avoid crashes. Also I suggest using current ChimeraX 1.6 instead of your 2 year old version 1.3.

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