Opened 4 years ago

Closed 4 years ago

#4746 closed defect (can't reproduce)

Crash in compute_cap

Reported by: stachowski.7@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000068cc (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\threading.py", line 306 in wait
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\threading.py", line 558 in wait
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\threading.py", line 1252 in run
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\threading.py", line 890 in _bootstrap

Current thread 0x00004414 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\chimerax\surface\cap.py", line 95 in compute_cap
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\chimerax\surface\cap.py", line 38 in show_surface_clip_caps
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\chimerax\surface\cap.py", line 28 in update_clip_caps
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\chimerax\core\updateloop.py", line 62 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\chimerax\core\updateloop.py", line 138 in _redraw_timer_callback
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.2.4\bin\lib\runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\kyest\\\Box\\\Shared-FLD\\\Manuscripts-FLD\\\01-Cre-Cryo-
> EM\\\Figures\\\Figure_3_Map+Models\\\Consistent_colored_models_maps\\\dimer_segmented_map.cxs

Opened cryosparc_P17_J335_002_segmented_map.mrc as #1, grid size 128,128,128,
pixel 1.8, shown at level 0.6, step 1, values float32  
Opened cryosparc_P17_J335_002_segmented_map.mrc 1 as #4.2, grid size
128,128,128, pixel 1.8, shown at level 0.5, step 1, values float32  
Opened cryosparc_P17_J335_002_segmented_map.mrc 2 as #4.3, grid size
128,128,128, pixel 1.8, shown at level 0.5, step 1, values float32  
Opened cryosparc_P17_J335_002_segmented_map.mrc 3 as #4.4, grid size
128,128,128, pixel 1.8, shown at level 0.5, step 1, values float32  
Showing cryosparc_P17_J335_002_segmented_map.seg - 4 regions, 4 surfaces  
Log from Fri Apr 30 10:48:42 2021

> size ballScale 0.225

Changed 0 ball scales  

> size stickRadius 0.15

Changed 0 bond radii  

> style ball

Changed 0 atom styles  

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> set bgColor white

> color byhetero

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\kyest\\\Box\\\Shared-FLD\\\Manuscripts-FLD\\\01-Cre-Cryo-
> EM\\\Map-
> Models\\\Yin+Yang+LoxP5\\\cryosparc_P17_J335_002_volume_map_sharp.mrc

Opened cryosparc_P17_J335_002_volume_map_sharp.mrc, grid size 128,128,128,
pixel 1.8, shown at level 0.291, step 1, values float32  

> open C:/Users/kyest/Box/Shared-FLD/Manuscripts-FLD/01-Cre-Cryo-EM/Map-
> Models/Yin+Yang+LoxP5/Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb

Summary of feedback from opening C:/Users/kyest/Box/Shared-FLD/Manuscripts-
FLD/01-Cre-Cryo-EM/Map-
Models/Yin+Yang+LoxP5/Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb  
---  
warning | Ignored bad PDB record found on line 12851  
END  
  
Chain information for
Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

>

Incomplete command: segmentation  

> help

Unknown command: segmentation help  

> help segmentation

> ui tool show "Segment Map"

> ui tool show "Fit to Segments"

QWindowsWindow::setGeometry: Unable to set geometry 1920x1132+0+23 (frame:
1936x1171-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1017+0+23 (frame: 1936x1056-8-8) margins: 8, 31, 8, 8
minimum size: 708x1132 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=724,1171
maxtrack=0,0)  

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.291228  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 5 region surfaces  
95 watershed regions, grouped to 5 regions  

> volume #1 level 0.4589

> close #3

> volume #1 level 0.4

> transparency 50

> transparency 0

> volume #1 level 0.45

> transparency 50

> volume #1 level 0.478

> volume #1 level 0.5

> transparency 0

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.500000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 6 region surfaces  
93 watershed regions, grouped to 6 regions  

> close #3

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.500000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Only showing 60 of 93 regions.  
Showing 60 of 93 region surfaces  
93 watershed regions, grouped to 93 regions  

> transparency 50

> transparency 0

Grouping with chains... making chain maps...  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 3349, in GroupRegionsByChains  
res, grid = self._sim_res_and_grid  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1135, in _sim_res_and_grid  
res, grid = self._sim_res.value, self._sim_grid_sp.value  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: invalid literal for int() with base 10: '4.5'  
  
ValueError: invalid literal for int() with base 10: '4.5'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
  
See log for complete Python traceback.  
  
Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.500000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 93 region surfaces  
93 watershed regions, grouped to 93 regions  
Grouping with chains... making chain maps...  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 3349, in GroupRegionsByChains  
res, grid = self._sim_res_and_grid  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1135, in _sim_res_and_grid  
res, grid = self._sim_res.value, self._sim_grid_sp.value  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: invalid literal for int() with base 10: '4.5'  
  
ValueError: invalid literal for int() with base 10: '4.5'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\composite.py", line 145, in _get_value  
return self.string_to_value(self._line_edit.text())  
  
See log for complete Python traceback.  
  
Grouping with chains... making chain maps...  
Grouping with chains... making map for chain 1/4 of mol 1/1  

> molmap #2/A 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 2/4 of mol 1/1  

> molmap #2/B 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 3/4 of mol 1/1  

> molmap #2/C 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 4/4 of mol 1/1  

> molmap #2/D 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping regions... 1/93  
Done - total 4 chains in 1 visible Molecules  

> volume #1 level 0.6398

> volume #3 level 0.5

No volumes specified  

> transparency 50

> close #3

> volume #1 level 0.5

> ui tool show "Segment Map"

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.500000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 93 region surfaces  
93 watershed regions, grouped to 93 regions  

> select #3

94 models selected  

> transparency sel 50

> select #1

2 models selected  

> transparency sel 0

> hide #!1 models

> show #!1 models

> ~select #1

Nothing selected  

> volume #1 level 0.3

> volume #1 level 0.5

> close #3

> volume #1 level 0.55

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.550000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 91 region surfaces  
91 watershed regions, grouped to 91 regions  

> select #3

92 models selected  

> transparency sel 50

> volume #1 level 0.5

> ~select #3

Nothing selected  

> select #3

92 models selected  

> transparency sel 0

> hide #!1 models

Grouping with chains... making chain maps...  
Grouping with chains... making map for chain 1/4 of mol 1/1  

> molmap #2/A 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 2/4 of mol 1/1  

> molmap #2/B 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 3/4 of mol 1/1  

> molmap #2/C 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 4/4 of mol 1/1  

> molmap #2/D 5.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping regions... 1/91  
Done - total 4 chains in 1 visible Molecules  

> graphics silhouettes true

> lighting soft

> hide #!2 models

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.500000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 93 region surfaces  
93 watershed regions, grouped to 93 regions  

> close #3

> show #!1 models

> volume #1 level 0.6

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.600000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 91 region surfaces  
91 watershed regions, grouped to 91 regions  

> select #3

92 models selected  

> transparency sel 50

> select #1

2 models selected  

> volume #1 level 0.5

> help segmentation

> close #3

> volume #1 level 0.65

> show #!2 models

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.650000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 91 region surfaces  
91 watershed regions, grouped to 91 regions  
Ungrouped to 0 regions  

> close #3

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.650000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 10 region surfaces  
91 watershed regions, grouped to 10 regions  

> close #3

Segmenting cryosparc_P17_J335_002_volume_map_sharp.mrc, density threshold
0.650000  
Showing cryosparc_P17_J335_002_volume_map_sharp.seg - 0 regions, 0 surfaces  
Showing 91 region surfaces  
91 watershed regions, grouped to 91 regions  
Grouping with chains... making chain maps...  
Grouping with chains... making map for chain 1/4 of mol 1/1  

> molmap #2/A 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 2/4 of mol 1/1  

> molmap #2/B 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 3/4 of mol 1/1  

> molmap #2/C 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 4/4 of mol 1/1  

> molmap #2/D 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping regions... 1/91  
Done - total 4 chains in 1 visible Molecules  

> hide #!2 models

> ~select #1

Nothing selected  

> select #3

5 models selected  

> transparency sel 50

> volume #1 level 0.5

> select #1

2 models selected  

> hide #!1 models

> show #!2 models

> hide #!2 models

> select #3

5 models selected  

> lighting soft

> transparency sel 0

> graphics silhouettes false

> graphics silhouettes true

> select clear

> ui tool show "Side View"

> save C:\Users\kyest\Desktop\image1.png supersample 3

> suntract #3.1+3.3 #1

Unknown command: suntract #3.1+3.3 #1  

> suntract #3.1 #1

Unknown command: suntract #3.1 #1  

> volume subtract #3.1 #1

volume subtract operation requires exactly two volumes  

> save C:/Users/kyest/Desktop/cryosparc_P17_J335_002_segmented_map.mrc models
> #1

> close #3

> open C:/Users/kyest/Desktop/cryosparc_P17_J335_002_segmented_map.mrc

Opened cryosparc_P17_J335_002_segmented_map.mrc, grid size 128,128,128, pixel
1.8, shown at level 0.291, step 1, values float32  

> volume #3 level 0.5

> close #3.1

> close #3

> show #!1 models

Segmenting cryosparc_P17_J335_002_segmented_map.mrc, density threshold
0.500000  
Showing cryosparc_P17_J335_002_segmented_map.seg - 0 regions, 0 surfaces  
Showing 93 region surfaces  
93 watershed regions, grouped to 93 regions  
Grouping with chains... making chain maps...  
Grouping regions... 1/93  
Done - total 0 chains in 0 visible Molecules  

> hide #!3 models

> show #!3 models

> show #!2 models

Grouping with chains... making chain maps...  
Grouping with chains... making map for chain 1/4 of mol 1/1  

> molmap #2/A 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 2/4 of mol 1/1  

> molmap #2/B 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 3/4 of mol 1/1  

> molmap #2/C 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 4/4 of mol 1/1  

> molmap #2/D 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping regions... 1/93  
Done - total 4 chains in 1 visible Molecules  

> close #3

> hide #!1 models

> show #!1 models

> volume #1 level 0.65

Segmenting cryosparc_P17_J335_002_segmented_map.mrc, density threshold
0.650000  
Showing cryosparc_P17_J335_002_segmented_map.seg - 0 regions, 0 surfaces  
Showing 91 region surfaces  
91 watershed regions, grouped to 91 regions  

> select #3

92 models selected  

> transparency sel 50

Grouping with chains... making chain maps...  
Grouping with chains... making map for chain 1/4 of mol 1/1  

> molmap #2/A 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 2/4 of mol 1/1  

> molmap #2/B 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 3/4 of mol 1/1  

> molmap #2/C 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping with chains... making map for chain 4/4 of mol 1/1  

> molmap #2/D 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Grouping regions... 1/91  
Done - total 4 chains in 1 visible Molecules  

> hide #!3 models

> select #1

2 models selected  

> transparency sel 50

> split #2

Split
Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb
(#2) into 4 models  
Chain information for
Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb
A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb
B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb
C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for
Yin_Yang_corrected_DNA_ISOLDE_noH_rsr46_ISOLDE_rsr52_ISOLDE_rsr_055_ISOLDE_trimmed_rsr059_final.pdb
D #2.4  
---  
Chain | Description  
D | No description available  
  

> hide #!1 models

> nucleotides slab

> style nucleic stick

Changed 2799 atom styles  

> cartoon style #2 modeHelix tube sides 20

> select clear

> hide pseudobonds

> show pseudobonds

> hide pseudobonds

> save C:\Users\kyest\Desktop\image2.png supersample 3

> show #!3 models

> show #!1 models

> hide #!3 models

> transparency #1.1 0

> volume #1 level 0.5

> color #1 near #2.1

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color zone #1 near #2.1

> volume #1 level 0.6072

> color zone #1 near #2.1 distance 2.5

> volume splitbyzone #1

> close #4.1

> volume #4.2 level 0.4037

> select clear

> color zone #1 near #2.2 distance 2.5

> show #!1 models

> color zone #1 near #2.2 distance 2.5 sharpEdges true

> volume splitbyzone #1

> close #5.1

> volume #5.2 level 0.4313

> volume #5.2 level 0.5

> close #4.2

> color zone #1 near #2.1 distance 2.5 sharpEdges true

> show #!1 models

> color zone #1 near #2.1/backbone distance 2.5 sharpEdges true

> volume #1 level 0.5839

> volume #1 level 0.6

> color zone #1 near #2.1 distance 2.5 sharpEdges true

> volume splitbyzone #1

> volume #6.1 color #00000002

> volume #6.1 color #00000019

> volume #6.1 color #00000009

> volume #6.1 color #00000063

> volume #6.1 color #5d5d5d63

> volume #6.1 color #5f5f5f63

> volume #6.1 color #62626263

> volume #6.1 color #66666663

> volume #6.1 color #6c6c6c63

> volume #6.1 color #6d6d6d63

> volume #6.1 color #6f6f6f63

> volume #6.1 color #70707063

> volume #6.1 color #71717163

> volume #6.1 color #78787863

> volume #6.1 color #82828263

> volume #6.1 color #8d8d8d63

> volume #6.1 color #91919163

> volume #6.1 color #aaaaaa63

> volume #6.1 color #b3b3b363

> volume #6.1 color #b9b9b963

> volume #6.1 color #c2c2c263

> volume #6.1 color #c7c7c763

> volume #6.1 color #cacaca63

> volume #6.1 color #cbcbcb63

> volume #6.1 color #cccccc63

> volume #6.1 color #cccccc01

> volume #6.1 color #cccccc0a

> volume #6.1 color #cccccc64

> volume #6.1 color #cccccc0a

> volume #6.1 color #cccccc01

> volume #6.1 color #cccccc06

> volume #6.1 color #cccccc41

> volume #6.1 color #cccccc06

> volume #6.1 color #cccccc02

> volume #6.1 color #cccccc19

> volume #6.1 color #cccccc

> close #6.1

> volume #6.2 level 0.5

> color zone #1 near #2.3-2.4 distance 2.5 sharpEdges true

> show #!1 models

> close #4

> hide #!5 models

> hide #!6 models

> color zone #1 near #2.3+2.4 dist 2.5 sharpEdges true

Invalid "near" argument: only initial part "#2.3" of atom specifier valid  

> color zone #1 near #2.3 distance 2.5 sharpEdges true

> help combine

No help found for 'combine'  

> help merge

No help found for 'merge'  

> color zone #1 near #2 distance 2.5 sharpEdges true

> color zone #1 near #2 distance 3 sharpEdges true

> color zone #1 near #2 distance 3.5 sharpEdges true

> volume splitbyzone #1

> close #4.1

> close #5

> close #6

> volume #4.2 level 0.5

> volume #4.3 level 0.5

> volume #4.4 level 0

> volume #4.4 level 0.1571

> hide #!2 models

> volume #4.4 level 0.4437

> volume #4.4 level 0.5

> surface dust #4

> save C:\Users\kyest\Desktop\image1.png supersample 3

> hide #!4 models

> show #!2 models

> save C:\Users\kyest\Desktop\image2.png supersample 3

> save C:\Users\kyest\Desktop\image3.png supersample 3

> hide #!2 models

> show #!4 models

> save C:\Users\kyest\Desktop\image4.png supersample 3

> save C:/Users/kyest/Desktop/dimer_segmented_map.cxs includeMaps true

——— End of log from Fri Apr 30 10:48:42 2021 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 461.09
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 81UH
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 17,095,249,920
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-isolde: 1.2.0
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.4
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.0
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in compute_cap

Reported by Kyle Stachowski

comment:2 by Tom Goddard, 4 years ago

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

This ChimeraX crash was computing the cap on holes of a surface when clipping. If it was an exceedingly large surface with lots of noise (e.g. a tomogram) possibly it exceeded the 32-bit array limits. I fixed that problem by switching to 64-bit indices when computing caps about 1 month ago, and that fix is in the ChimeraX daily build but did not make it into ChimeraX 1.2.

I don't have any other theory about how the cap C++ code might crash so will have to wait and see if this crash is ever reported with the daily build which uses the 64-bit indices.

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