Opened 4 years ago

Closed 4 years ago

#6467 closed defect (can't reproduce)

Crash after opening sessions containing volumes

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

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-166-generic-x86_64-with-glibc2.27
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

Thread 0x00007fbf1bf55700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007fc14e68b740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/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 22Feb25_2A3_fib1_33_mc__bin2.mrc

Opened 22Feb25_2A3_fib1_33_mc__bin2.mrc as #1, grid size 2048,2048,512, pixel
4.2, shown at step 1, values float32  

> volume scale #1 factor -1

Opened 22Feb25_2A3_fib1_33_mc__bin2.mrc scaled as #2, grid size 2048,2048,512,
pixel 4.2, shown at step 1, values float32  

> close #2

> close #1

> open
> /mount/local4/alyokom/atg9/22Feb25/tomograms/22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc
> /mount/local4/alyokom/atg9/22Feb25/tomograms/22Feb25_2A3_fib1_12_mc__bin4_preproc_invert.mrc

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc as #1.1, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at level 2.34, step 4, values float32  
Opened 22Feb25_2A3_fib1_12_mc__bin4_preproc_invert.mrc as #1.2, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at level 2.4, step 4, values float32  

> volume #1.2 style image region 0,0,124,1023,1023,124 step 1 showOutlineBox
> true

> volume #1.2 region 0,0,178,1023,1023,178

> volume scale #1.1 factor -1

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc scaled as #2, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at step 1, values float32  

> volume scale #1.2 factor -1

Opened 22Feb25_2A3_fib1_12_mc__bin4_preproc_invert.mrc scaled as #3, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at step 1, values float32  

> close #1.1

> close #1

> hide #!3 models

> hide #!2 models

> show #!3 models

> volume #3 level -1.37,0 level 2.589,0.8 level 3,1

> volume #3 color #ffffb3 color #babdb6 color #ffffb3

> volume #3 color #ffffb3 color #888a85 color #ffffb3

> volume #3 color #ffffb3 color #888a85 color #888a85

> volume #3 level -1.37,0 level 2.589,0.8 level 3,1

> volume #3 color #babdb6 color #888a85 color #888a85

> view orient

> ui tool show "Side View"

> close #3

> view

> view orient

> volume #2 style image region 0,0,124,1023,1023,124 step 1 showOutlineBox
> true

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

> ui tool show "Segment Map"

> volume #2 region 0,0,0,1023,1023,249 step 4

> volume #2 style surface region 0,0,0,1023,1023,249 step 4

> volume #2 change image level -1.465,0 level 2.817,0.8 level 3,1

> volume #2 level 1.93

> volume #2 level 1.682

> volume #2 step 8

> volume #2 step 4

> volume #2 level 1.599

> volume #2 level 1.526

> volume gaussian #2 sDev 4

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc scaled gaussian as #1,
grid size 1024,1024,250, pixel 8.4,8.4,8.4, shown at step 1, values float32  

> volume #1 style image region 0,0,124,1023,1023,124 step 1

> volume #!1 step 1

> view orient

> volume #1 region 0,0,0,1023,1023,249 step 4

> volume #1 style surface region 0,0,0,1023,1023,249 step 4

> volume #1 change image level -1.383,0 level 2.639,0.8 level 3,1

> volume #1 level 1.967

> volume #1 level 1.49

> volume #1 step 2

> volume #1 level 1.356

> view orient

> view

Segmenting 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc scaled gaussian,
density threshold 1.355616  
Only showing 600 of 27976 regions.  
Showing 600 of 27976 region surfaces  
381675 watershed regions, grouped to 27976 regions  
Showing 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert scaled gaussian.seg -
27976 regions, 600 surfaces  

> hide #!3 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> volume #2 style image region 0,0,124,1023,1023,124 step 1

> show #!3 models

> volume #2 region 0,0,169,1023,1023,169

Segmenting 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc scaled gaussian,
density threshold 1.355616  
Only showing 1200 of 3538 regions.  
Showing 1200 of 3538 region surfaces  
381675 watershed regions, grouped to 3538 regions  
Showing 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert scaled gaussian.seg - 3538
regions, 1200 surfaces  

> hide #!2 models

> close #3

> volume #1 region 0,0,0,1023,1023,249

> ui mousemode right "map eraser"

> volume erase #1 center -179.26,1101.8,91.221 radius 1228.3

> volume erase #1 center -160.09,1827,85.477 radius 1228.3

> volume erase #1 center 918.03,813.3,178.23 radius 1228.3

> volume erase #1 center 30.547,574.91,112.55 radius 1228.3

> ui mousemode right "map eraser"

> hide #3 models

> volume #1 style image region 0,0,124,1023,1023,124 step 1

> volume #1 region 0,0,0,1023,1023,0

> close #1

> view orient

> ui tool show "Side View"

> view

> close #2

> open /home/alyokom/Dropbox/Tomo/ER_Auto_site1.mrc

Opened ER_Auto_site1.mrc as #1, grid size 427,373,164, pixel 8.4,8.4,8.4,
shown at level 2.42, step 2, values float32  

> volume #1 style image region 0,0,80,426,372,80 step 1 showOutlineBox true

> volume #1 region 0,0,163,426,372,163

> movie record

> volume #1 region 0,0,163,426,372,163

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> open
> /home/alyokom/Dropbox/Tomo/22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc as #2, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at level 2.34, step 4, values float32  

> volume #1 level -1.412,0 level 2.555,0.8 level 3,1

> close #1

> volume #2 style image region 0,0,124,1023,1023,124 step 1 showOutlineBox
> true

> close #2

> open
> /home/alyokom/Dropbox/Tomo/22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc
> format mrc

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc as #1, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at level 2.34, step 4, values float32  

> volume #1 style image region 0,0,124,1023,1023,124 step 1 showOutlineBox
> true

> volume #1 planes z,10,

Invalid "planes" argument: Planes arguments after axis must be numbers  

> volume #1 planes z,10,180,1,5

> movie record

> volume #1 planes z,10,180,1,5

> wait 240

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> movie record

> volume #1 planes z,10,180,1,5

> wait 190

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> volume #1 region 0,0,106,1023,1023,110

> volume #1 region 0,0,108,1023,1023,108 step 1

> open emdb:22586

Summary of feedback from opening 22586 fetched from emdb  
---  
note | Fetching compressed map 22586 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22586/map/emd_22586.map.gz  
  
Opened emdb 22586 as #2, grid size 496,496,496, pixel 0.712, shown at level
0.0326, step 2, values float32  

> volume gaussian #2 sDev 5

Opened emdb 22586 gaussian as #3, grid size 496,496,496, pixel 0.712, shown at
step 1, values float32  

> view

> close #2

> volume #3 level 0.008069

> volume #3 step 4

> volume #3 level 0.00263

> volume #3 region 0,0,0,495,495,495

> volume #1 level -1.491,0 level 2.656,0.8 level 3,1

> select #3

2 models selected  

> volume #3 region 0,0,0,495,495,495

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-395.7,0,1,0,-1952.1,0,0,1,293.28

> ~select #3

Nothing selected  

> select #3

2 models selected  

> view matrix models #3,1,0,0,-340.63,0,1,0,-2021.3,0,0,1,311.25

> view matrix models
> #3,0.99979,0.0176,-0.010528,-341.78,-0.016092,0.99147,0.1293,-2041.4,0.012714,-0.1291,0.99155,333.98

> view matrix models
> #3,0.99979,0.0176,-0.010528,-172.47,-0.016092,0.99147,0.1293,-2326.3,0.012714,-0.1291,0.99155,399.55

> view matrix models
> #3,0.99979,0.0176,-0.010528,-173.35,-0.016092,0.99147,0.1293,-2319.9,0.012714,-0.1291,0.99155,398.51

> view matrix models
> #3,0.99979,0.0176,-0.010528,-436.37,-0.016092,0.99147,0.1293,-2111.5,0.012714,-0.1291,0.99155,-97.207

> view matrix models
> #3,0.99979,0.0176,-0.010528,-436.77,-0.016092,0.99147,0.1293,-2070.5,0.012714,-0.1291,0.99155,-157.22

> view matrix models
> #3,0.99979,0.0176,-0.010528,-204.34,-0.016092,0.99147,0.1293,-2202.9,0.012714,-0.1291,0.99155,-233.75

> view matrix models
> #3,0.99979,0.0176,-0.010528,-210.37,-0.016092,0.99147,0.1293,-2190.5,0.012714,-0.1291,0.99155,-257.64

> volume copy #2 #3

Opened emdb 22586 gaussian copy as #2, grid size 496,496,496, pixel 0.712,
shown at step 1, values float32  

> show #!3 models

> hide #!2 models

> show #!2 models

> ~select #3

Nothing selected  

> select #3

2 models selected  

> view matrix models
> #3,0.99979,0.0176,-0.010528,-124.86,-0.016092,0.99147,0.1293,-2467.3,0.012714,-0.1291,0.99155,-320.72

> volume copy #2 #4

Opened emdb 22586 gaussian copy as #4, grid size 496,496,496, pixel 0.712,
shown at step 1, values float32  

> volume copy #2 #5

Opened emdb 22586 gaussian copy as #5, grid size 496,496,496, pixel 0.712,
shown at step 1, values float32  

> volume copy #2 #6

Opened emdb 22586 gaussian copy as #6, grid size 496,496,496, pixel 0.712,
shown at step 1, values float32  

> select #4

2 models selected  

> ~select #3

2 models selected  

> view matrix models
> #4,0.99979,0.0176,-0.010528,3148.5,-0.016092,0.99147,0.1293,-786.28,0.012714,-0.1291,0.99155,-387.04

> select #5

2 models selected  

> ~select #4

2 models selected  

> view matrix models
> #5,0.99979,0.0176,-0.010528,-462.45,-0.016092,0.99147,0.1293,-2788.4,0.012714,-0.1291,0.99155,-319.13

> ~select #5

Nothing selected  

> select #6

2 models selected  

> view matrix models
> #6,0.99979,0.0176,-0.010528,-256.94,-0.016092,0.99147,0.1293,-2186.8,0.012714,-0.1291,0.99155,-252.49

> show #!2 models

> view matrix models
> #6,0.99979,0.0176,-0.010528,-12.944,-0.016092,0.99147,0.1293,-1956.6,0.012714,-0.1291,0.99155,-243.37

> volume copy #2 #7

Opened emdb 22586 gaussian copy as #7, grid size 496,496,496, pixel 0.712,
shown at step 1, values float32  

> select #7

2 models selected  

> ~select #6

2 models selected  

> show #!2 models

> view matrix models
> #7,0.99979,0.0176,-0.010528,-953.68,-0.016092,0.99147,0.1293,-1790.9,0.012714,-0.1291,0.99155,-126.32

> volume #1 region 0,0,0,1023,1023,249 step 4

> volume #1 style surface region 0,0,0,1023,1023,249 step 4

> volume #1 level 1.565

> volume #1 step 8

> view matrix models
> #7,0.99979,0.0176,-0.010528,-961.16,-0.016092,0.99147,0.1293,-1776.6,0.012714,-0.1291,0.99155,-130.26

> view matrix models
> #7,0.99979,0.0176,-0.010528,-955.43,-0.016092,0.99147,0.1293,-1824.5,0.012714,-0.1291,0.99155,-126.64

> ~select #7

Nothing selected  

> ui mousemode right select

> volume fit #2 #1

Expected a density maps specifier or a keyword  

> volume #2 fit #1

Expected a keyword  

> ui tool show "Fit in Map"

Fit map emdb 22586 gaussian copy in map
22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc using 10656300 points  
correlation = 0.4909, correlation about mean = 0.05025, overlap = 4.454e+04  
steps = 224, shift = 161, angle = 90.8 degrees  
  
Position of emdb 22586 gaussian copy (#2) relative to
22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.02983884 0.43683416 -0.89904703 204.22591414  
-0.25696524 0.86586485 0.42923993 -2230.88299102  
0.96595989 0.24383186 0.08641479 -361.90013240  
Axis -0.09277382 -0.93320543 -0.34716084  
Axis point 7.93552299 0.00000000 443.90886397  
Rotation angle (degrees) 92.22246482  
Shift along axis 2188.56285122  
  

> select #1

3 models selected  

> volume #1 style image region 0,0,120,1023,1023,120 step 2

> ui mousemode right select

> ui mousemode right rotate

> view

> view orient

> select clear

> select #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.029839,0.43683,-0.89905,53.75,-0.25697,0.86586,0.42924,-2155.6,0.96596,0.24383,0.086415,-358.62

> select clear

> ~select #2

Nothing selected  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> movie record

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!7 models

> show #!6 models

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> movie record

> wait 40

> display #2

> wait 10

> display #3

> wait 10

> display #4-8

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> movie record

> wait 40

> display #2

> wait 10

> display #3

> wait 10

> display #4-8

> waot 40 movie encode

Unknown command: waot 40 movie encode  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> movie record

Already recording a movie  

> movie stop

> movie record

> wait 40

> display #2

> wait 10

> display #3

> wait 10

> display #4-8

> wait 40

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!2 models

> hide #!6 models

> hide #!7 models

> movie record

> wait 40

> display #2

> wait 10

> display #3

> wait 10

> display #4-8

> wait 40

> movie encode

Movie saved to /home/alyokom/Desktop/movie.mp4  
  

> hide #!3 models

> hide #!2 models

> hide #!5 models

> hide #!4 models

> hide #!6 models

> hide #!7 models

> open emdb:10779

Summary of feedback from opening 10779 fetched from emdb  
---  
note | Fetching compressed map 10779 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10779/map/emd_10779.map.gz  
  
Opened emdb 10779 as #8, grid size 320,320,320, pixel 1.39, shown at level
0.0562, step 2, values float32  

> select #8

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,-2806.5,0,1,0,-1934.8,0,0,1,39.709

> close #8

> open emdb:2411

Summary of feedback from opening 2411 fetched from emdb  
---  
note | Fetching compressed map 2411 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-2411/map/emd_2411.map.gz  
  
Opened emdb 2411 as #8, grid size 256,256,256, pixel 6.4, shown at level 22.8,
step 1, values float32  

> view

> view orient

> select #8

2 models selected  

> view matrix models #8,1,0,0,-2640.3,0,1,0,-1611.2,0,0,1,0

> view matrix models #8,1,0,0,-2650.7,0,1,0,-1632,0,0,1,0

> ~select #8

Nothing selected  

> view

> view orient

> hide #!8 models

> show #!8 models

> select #8

2 models selected  

> view matrix models #8,1,0,0,-2543.2,0,1,0,-1649.9,0,0,1,0

> view matrix models #8,1,0,0,-2550.4,0,1,0,-1635.6,0,0,1,0

> view matrix models #8,1,0,0,-2550.4,0,1,0,-1632,0,0,1,0

> view matrix models
> #8,0.99966,0.00072003,-0.026209,-2550.4,0.0004234,0.99905,0.043595,-1632,0.026216,-0.043591,0.99871,2.0461e-05

> view matrix models
> #8,0.99966,0.00072003,-0.026209,-2546.8,0.0004234,0.99905,0.043595,-1639.2,0.026216,-0.043591,0.99871,2.0461e-05

> ~select #8

Nothing selected  

> select #8

2 models selected  

> view matrix models
> #8,0.99966,0.00072003,-0.026209,-2556.8,0.0004234,0.99905,0.043595,-1643.4,0.026216,-0.043591,0.99871,-3.729

> view matrix models
> #8,0.99966,0.00072003,-0.026209,-2572.1,0.0004234,0.99905,0.043595,-1642.5,0.026216,-0.043591,0.99871,-241.4

> ~select #8

Nothing selected  

> view orient

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> select #8

2 models selected  

> view matrix models
> #8,0.99966,0.00072003,-0.026209,-2552,0.0004234,0.99905,0.043595,-1662.7,0.026216,-0.043591,0.99871,-243.52

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.99975,-0.015629,0.016269,-2552,0.017238,0.99443,-0.10397,-1662.7,-0.014554,0.10423,0.99445,-243.52

> ~select #8

Nothing selected  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> volume scale #1 factor -1

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc scaled as #9, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at step 1, values float32  
Fit map emdb 2411 in map 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc
scaled using 167722 points  
correlation = 0, correlation about mean = 0, overlap = 0  
steps = 24, shift = 0, angle = 0 degrees  
  
Position of emdb 2411 (#8) relative to
22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc scaled (#9) coordinates:  
Matrix rotation and translation  
0.99974550 -0.01562864 0.01626917 -2551.95509759  
0.01723754 0.99443073 -0.10397303 -1662.69987927  
-0.01455361 0.10422701 0.99444704 -243.51975349  
Axis 0.97737357 0.14469438 0.15428688  
Axis point 0.00000000 -2407.06354203 -12004.53749847  
Rotation angle (degrees) 6.11416870  
Shift along axis -2772.36869557  
  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> select #8

2 models selected  

> view matrix models
> #8,0.99686,-0.014814,0.077842,-2552,0.013481,0.99975,0.017626,-1662.7,-0.078084,-0.016522,0.99681,-243.52

> view

> view orient

> hide #!8 models

> view matrix models
> #8,0.96755,-0.078605,-0.24015,-2224.3,-0.056442,0.85914,-0.50862,-1009,0.2463,0.50567,0.82682,-1836

> ui mousemode right "move planes"

> volume #1 region 0,0,191,1023,1023,191

> volume #1 region 0,0,238,1023,1023,238

> volume #1 planes z,100,180,1,5

> volume #1 region 0,0,188,1023,1023,188 step 2

> volume #1 planes z,100,180,1,5

> hide #!1 models

> show #!1 models

> volume #1 colorMode opaque8 imageMode "box faces"

> volume #1 planes z,100,180,1,5

> volume #1 colorMode auto8 imageMode "full region"

> close #9

> volume #1 planes z,100,180,1,5

> volume #1 planes z,100,180,2,5

> volume #1 planes z,10,180,2,5

> volume #1 region 0,0,188,1023,1023,188 step 2

> volume #1 planes z,10,180,2,5

> save /home/alyokom/Dropbox/Tomo/fittings.cxs

> select #2

2 models selected  

> close #2-7

> show #!8 models

> hide #!8 models

> volume #1 planes z,10,180,2,5

> close #8

> volume #1 region 0,0,188,1023,1023,188 step 2

> volume #1 planes z,10,180,2,5

> open /home/alyokom/Dropbox/Tomo/fittings.cxs

Opened 22Feb25_2A3_fib1_33_mc__bin4_preproc_invert.mrc as #1, grid size
1024,1024,250, pixel 8.4,8.4,8.4, shown at step 4, values float32  
Opened emdb 22586 gaussian as #3, grid size 496,496,496, pixel 0.712, shown at
level 0.00263, step 4, values float32  
Opened emdb 22586 gaussian copy as #2, grid size 496,496,496, pixel 0.712,
shown at level 0.00263, step 1, values float32  
Opened emdb 22586 gaussian copy as #4, grid size 496,496,496, pixel 0.712,
shown at level 0.00263, step 1, values float32  
Opened emdb 22586 gaussian copy as #5, grid size 496,496,496, pixel 0.712,
shown at level 0.00263, step 1, values float32  
Opened emdb 22586 gaussian copy as #6, grid size 496,496,496, pixel 0.712,
shown at level 0.00263, step 1, values float32  
Opened emdb 22586 gaussian copy as #7, grid size 496,496,496, pixel 0.712,
shown at level 0.00263, step 1, values float32  
Opened emdb 2411 as #8, grid size 256,256,256, pixel 6.4, shown at level 22.8,
step 1, values float32  
opened ChimeraX session  


===== 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 430.26
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: Z10PE-D8 WS
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 56 Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz
Cache Size: 35840 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        7.9G        116G        173M        1.7G        116G
	Swap:          127G        3.5G        124G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)	
	Subsystem: eVga.com. Corp. GP102 [GeForce GTX 1080 Ti] [3842:5390]	
	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: 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-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 pett, 4 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash after opening sessions containing volumes

Seems like not enough info to reproduce?

comment:2 by Tom Goddard, 4 years ago

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

After several hundred commands the last command opened a session file. Then it crashed in the Qt event loop. Nothing to help debug this.

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