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#8235 closed defect (nonchimerax)

Crash saving image in Pillow, ChimeraX 1.3, Linux 3.10

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

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f6138334740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/ImageFile.py", line 518 in _save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/PngImagePlugin.py", line 1349 in _save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/Image.py", line 2235 in save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/image_formats/save.py", line 123 in save_image
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/image_formats/__init__.py", line 45 in save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 89 in provider_save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 512 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 1254 in save_image
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 327 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 408 in run_shortcut
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 390 in try_shortcut
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 1334 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/__init__.py", line 52 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1284 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 381 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 165 in callback
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== 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  

> open /data/PRC26U1T_1G4L_20220317/Phenix_final/final_figure.cxs format
> session

Opened 1G4_RNA.mrc as #1.1, grid size 300,300,300, pixel 1.06, shown at level
0.0164, step 1, values float32  
Opened Body1_postproposs_RNAandOverlapping_removed.mrc as #1.2, grid size
300,300,300, pixel 1.06, shown at level 0.015, step 1, values float32  
Opened Body2_postproposs_RNAandOverlapping_removed.mrc as #1.3, grid size
300,300,300, pixel 1.06, shown at level 0.0164, step 1, values float32  
opened ChimeraX session  

> lighting intensity 0.25

> material dull

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> view

> lighting intensity 0.2

> lighting intensity 0.25

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> open
> /data/PRC26U1T_1G4L_20220317/Phenix_final/Body1_final_final3_real_space_refined_028.pdb
> /data/PRC26U1T_1G4L_20220317/Phenix_final/Body2_final_final3_real_space_refined_027.pdb
> /data/PRC26U1T_1G4L_20220317/Phenix_final/RNA_G4_aligned.pdb

Chain information for Body1_final_final3_real_space_refined_028.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  
Chain information for Body2_final_final3_real_space_refined_027.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  
RNA_G4_aligned.pdb title:  
Structure of stacked G-quadruplex formed by human terra sequence In potassium
solution [more info...]  
  
Chain information for RNA_G4_aligned.pdb #4  
---  
Chain | Description  
A B | RNA (5'-R(*GP*GP*GP*up*up*ap*GP*GP*GP*U)-3')  
  

> hide #!1 models

> hide #2.2 models

> hide #3.2 models

> show cartoons

> hide atoms

> hide surfaces

> select #2/A:31

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

244 atoms, 246 bonds, 39 residues, 1 model selected  

> select up

3434 atoms, 3498 bonds, 521 residues, 1 model selected  

> select up

12550 atoms, 12851 bonds, 1853 residues, 1 model selected  

> select up

25732 atoms, 26382 bonds, 3722 residues, 4 models selected  

> select up

25732 atoms, 26382 bonds, 3722 residues, 4 models selected  

> select down

12550 atoms, 12851 bonds, 1853 residues, 1 model selected  

> select down

3434 atoms, 3498 bonds, 521 residues, 1 model selected  

> select down

244 atoms, 246 bonds, 39 residues, 1 model selected  

> select down

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select down

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select down

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #2

12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected  

> rainbow sel

> color sel bychain

> show sel atoms

> style sel stick

Changed 12550 atom styles  

> style sel ball

Changed 12550 atom styles  

> style sel sphere

Changed 12550 atom styles  

> style sel stick

Changed 12550 atom styles  

> style sel ball

Changed 12550 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> hide sel atoms

> ~select #2

Nothing selected  

> select #4

592 atoms, 638 bonds, 18 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 592 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 592 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 592 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel slab

> style nucleic & sel stick

Changed 592 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel tube/slab shape muffler

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> nucleotides sel stubs

> nucleotides sel tube/slab shape box

> nucleotides sel slab

> style nucleic & sel stick

Changed 592 atom styles  

> nucleotides sel tube/slab shape box

> color sel bynucleotide

> ui tool show "Color Actions"

> color sel orange

> save /data/PRC26U1T_1G4L_20220317/Phenix_final/final_figure.cxs

> select #2/A#3/A

6862 atoms, 6990 bonds, 68 pseudobonds, 1042 residues, 6 models selected  

> select #2/B#3/B

5844 atoms, 5964 bonds, 20 pseudobonds, 866 residues, 4 models selected  

> color sel forest green

> color sel green

> color sel forest green

> select #2/C#3/C

5255 atoms, 5401 bonds, 732 residues, 2 models selected  

> color sel cyan

> color sel deep sky blue

> color sel cyan

> select #2/D#3/D

5444 atoms, 5612 bonds, 2 pseudobonds, 784 residues, 4 models selected  

> color sel yellow

> color sel purple

> color sel cornflower blue

> color sel medium purple

> select #2/E#3/E

358 atoms, 362 bonds, 62 residues, 2 models selected  

> color sel magenta

> select #2/F#3/F

1377 atoms, 1415 bonds, 2 pseudobonds, 218 residues, 4 models selected  

> color sel red

> help help:user/findseq.html

> select #2

12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected  

> ui tool show "Blast Protein"

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #3/A

Alignment identifier is 1  

> select #2/A:22-23 #3/A:22-23

20 atoms, 18 bonds, 4 residues, 2 models selected  

> select #2/A:22-124 #3/A:22-124

1381 atoms, 1407 bonds, 206 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [1-103] RMSD: 144.512  
  

> select #2/A:741 #3/A:741

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:598-741 #3/A:598-741

2047 atoms, 2089 bonds, 288 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [370-513] RMSD: 59.124  
  

> select #2/A:742 #3/A:742

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:23-742 #3/A:23-742

6838 atoms, 6980 bonds, 12 pseudobonds, 1026 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [2-514] RMSD: 95.556  
  

> select #2/A:712-742 #3/A:712-742

444 atoms, 450 bonds, 62 residues, 2 models selected  

> select #2/A:577-742 #3/A:577-742

2336 atoms, 2384 bonds, 332 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [349-514] RMSD: 55.917  
  

> color sel blue

> select #2/A:577 #3/A:577

14 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2/A:540-577 #3/A:540-577

534 atoms, 544 bonds, 76 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [312-349] RMSD: 26.025  
  

> color sel blue

> select #2/A:540 #3/A:540

14 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2/A:481-540 #3/A:481-540

312 atoms, 322 bonds, 2 pseudobonds, 46 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [290-312] RMSD: 49.257  
  

> color sel blue

> select #2/A:479-480 #3/A:479-480

20 atoms, 18 bonds, 4 residues, 2 models selected  

> select #2/A:479-481 #3/A:479-481

30 atoms, 28 bonds, 6 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [288-290] RMSD: 110.420  
  

> color sel blue

> select #2/A:481 #3/A:481

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:481-522 #3/A:481-522

54 atoms, 50 bonds, 2 pseudobonds, 10 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [290-294] RMSD: 73.704  
  

> select #2/A:482-520 #3/A:482-520

20 atoms, 16 bonds, 2 pseudobonds, 4 residues, 4 models selected  

> select #2/A:482-524 #3/A:482-524

84 atoms, 82 bonds, 2 pseudobonds, 12 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [291-296] RMSD: 52.564  
  

> select #2/A:520 #3/A:520

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:520-525 #3/A:520-525

98 atoms, 100 bonds, 12 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [292-297] RMSD: 31.845  
  

> select #2/A:481-482 #3/A:481-482

20 atoms, 18 bonds, 4 residues, 2 models selected  

> select #2/A:274-482 #3/A:274-482

1731 atoms, 1775 bonds, 2 pseudobonds, 264 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [160-291] RMSD: 91.364  
  

> color sel hot pink

> select #2/A:273 #3/A:273

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:269-273 #3/A:269-273

60 atoms, 58 bonds, 10 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [155-159] RMSD: 103.180  
  

> select #2/A:273 #3/A:273

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:250-273 #3/A:250-273

224 atoms, 228 bonds, 2 pseudobonds, 36 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [142-159] RMSD: 104.862  
  

> select #2/A:257 #3/A:257

14 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2/A:257-277 #3/A:257-277

266 atoms, 272 bonds, 42 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [143-163] RMSD: 100.469  
  

> color sel hot pink

> select #2/A:250 #3/A:250

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:22-250 #3/A:22-250

1769 atoms, 1789 bonds, 6 pseudobonds, 284 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [1-142] RMSD: 141.653  
  

> color sel gold

> select #2/A:742 #3/A:742

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #2/A:577-742 #3/A:577-742

2336 atoms, 2384 bonds, 332 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [349-514] RMSD: 55.917  
  

> select #3

12590 atoms, 12893 bonds, 46 pseudobonds, 1851 residues, 3 models selected  

> select #2

12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected  

> ~select #2

Nothing selected  

> show #!1 models

> hide #!1 models

> ui tool show "Surface Color"

> show #!1 models

> color radial #1.1.1 palette #ff0000:#ffffff:#0000ff

> color single #1.1.1

> ui tool show "Color Zone"

> color zone #1.2 near #2 distance 6.38

> color zone #1.2 near #2 distance 17.05

> color zone #1.2 near #2 distance 16.94

> color zone #1.2 near #2 distance 17.05

> color zone #1.2 near #2 distance 16.94

> color zone #1.2 near #2 distance 11.33

> color zone #1.2 near #2 distance 11.25

> color zone #1.2 near #2 distance 11.17

> color zone #1.2 near #2 distance 11.24

> color zone #1.2 near #2 distance 8.85

> color zone #1.2 near #2 distance 8.75

> color single #1.2

> color zone #1.2 near #2 distance 6

> color zone #1.2 near #2 distance 8

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #3/A

Alignment identifier is 1  

> hide #!1 models

> lighting depthCue false

> open
> /data/PRC26U1T_1G4L_20220317/Phenix_final/Body1_final_final1_real_space_refined_023-coot-1.pdb

Chain information for Body1_final_final1_real_space_refined_023-coot-1.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide atoms

> hide #!5 models

> show #!5 models

> show cartoons

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!5 models

> close #5

> show #!1 models

> color zone #1.2 near #2 distance 7

> lighting depthCue false

> volume #1.2 level 0.01512

> volume #1.2 level 0.015

> volume #1.2 level 0.0155

> volume #1.2 level 0.015

> select #1.2

2 models selected  

> select #1

7 models selected  

> ~select #1

Nothing selected  

> select #1.2

2 models selected  

> select #1

7 models selected  

> ~select #1

Nothing selected  

> volume #1.2 level 0.0155

> volume #1.2 level 0.015

> color zone #1.2 near #2 distance 6

> lighting depthCue false

> color zone #1.3 near #3 distance 6.38

> volume #1.3 level 0.0164

> color zone #1.3 near #3 distance 7

> lighting depthCue false

> color zone #1.3 near #3 distance 8

> lighting depthCue false

> color zone #1.1 near #4 distance 6.38

> color zone #1.1 near #4 distance 8

> color zone #1.1 near #4 distance 9

> hide #!2 models

> hide #!3 models

> hide #4 models

> lighting intensity 0.4

> lighting intensity 0.3

> color #1 #eeeeec models transparency 0

> color #1 white models transparency 0

> color #1 #d3d7cf models transparency 0

> color zone #1.1 near #4 distance 9

> color zone #1.2 near #2 distance 6.38

> ui tool show "Hide Dust"

> surface dust #1.1 size 1.06

> surface dust #1.2 size 6.13

> surface dust #1.2 size 11.03

> select #2

12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected  

> ~select #2

Nothing selected  

> select #2

12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected  

> ~select #2

Nothing selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> surface dust #1.2 size 11.13

> surface dust #1.1 size 5.97

> color zone #1.3 near #3 distance 6.38

> color zone #1.3 near #3 distance 7.97

> color zone #1.3 near #3 distance 7

> lighting intensity 0.3

> surface dust #1.3 size 14.46

> surface dust #1.3 size 8.41

> save /data/PRC26U1T_1G4L_20220317/Phenix_final/final_figure_map.cxs

> view

> save /home/spuser/Desktop/image1.png supersample 3


===== 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 NVIDIA 470.63.01
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 96 Intel(R) Xeon(R) Gold 5220R CPU @ 2.20GHz
Cache Size: 36608 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           251G         11G        238G         40M        1.7G        239G
	Swap:           31G          0B         31G

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: Super Micro Computer Inc Device [15d9:096d]	
	Kernel driver in use: ast
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: 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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    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
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    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
    line-profiler: 3.3.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Input/Output
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash saving image

comment:2 by Tom Goddard, 3 years ago

Resolution:	→ nonchimerax
Status:	assigned → closed
Summary:	Crash saving image → Crash saving image in Pillow, ChimeraX 1.3, Linux 3.10

Crash reported several times before in Pillow saving image file, always old ChimeraX 1.3 and old Linux 1.3. Probably fixed in current ChimeraX Pillow.

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