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Opened 4 years ago
Closed 4 years ago
#6467 closed defect (can't reproduce)
Crash after opening sessions containing volumes
| Reported by: | 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 , 4 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash after opening sessions containing volumes |
comment:2 by , 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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Seems like not enough info to reproduce?