![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7136 closed defect (can't reproduce)
Crash deleting some tool's interface
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
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 0x0000000202de8600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 2700000,
"procLaunch" : "2022-06-20 18:42:57.0965 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 66580130709611,
"coalitionID" : 187786,
"osVersion" : {
"train" : "macOS 12.3.1",
"build" : "21E258",
"releaseType" : "User"
},
"captureTime" : "2022-06-20 18:53:42.0645 +0100",
"incident" : "521A9AC9-1A01-466F-BA2F-63151408A5E5",
"bug_type" : "309",
"pid" : 85761,
"procExitAbsTime" : 66595607906209,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"747C3F2E-A655-5C1F-A8FC-C212BAFBB3C9","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CA582E41-11B6-6235-261E-4B953049E08A",
"wakeTime" : 28640,
"sleepWakeUUID" : "AD5C3827-F0D9-4245-8A8E-F389F41E1C01",
"sip" : "enabled",
"vmRegionInfo" : "0x7fb9be12a9b is not in any region. Bytes after previous region: 8296197073564 Bytes before following region: 131658498889061\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x7f49bdf00000 BYTES\n MALLOC_TINY 7fb9bdf00000-7fb9be000000 [ 1024K] rw-\/rwx SM=PRV ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0xc00007fb9be12a9b","rawCodes":[1,-4611677241193977189],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0xc00007fb9be12a9b -> 0x000007fb9be12a9b (possible pointer authentication failure)"},
"ktriageinfo" : "VM - pmap_enter failed with resource shortage\n",
"vmregioninfo" : "0x7fb9be12a9b is not in any region. Bytes after previous region: 8296197073564 Bytes before following region: 131658498889061\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x7f49bdf00000 BYTES\n MALLOC_TINY 7fb9bdf00000-7fb9be000000 [ 1024K] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== 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
> /Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/cryosparc_P8_J39__localfilter.mrc
> format mrc
Opened cryosparc_P8_J39__localfilter.mrc as #1, grid size 128,128,128, pixel
1.96, shown at level 0.694, step 1, values float32
> set bgColor white
> transparency 50
> lighting flat
> transparency 0
> transparency 50
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Pta1/Pta1
> 1-322 fit.pdb"
Chain information for Pta1 1-322 fit.pdb #2
---
Chain | Description
A | No description available
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Swd2.2
> AlphaFold.pdb" format pdb
Swd2.2 AlphaFold.pdb title:
Alphafold V2.0 prediction for uncharacterized WD repeat-containing protein
C824.04 (Q9UT39) [more info...]
Chain information for Swd2.2 AlphaFold.pdb #3
---
Chain | Description | UniProt
A | uncharacterized WD repeat-containing protein C824.04 | YIQ4_SCHPO
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Ssu72
> AlphaFold.pdb" format pdb
Ssu72 AlphaFold.pdb title:
Alphafold V2.0 prediction for RNA polymerase II subunit A C-terminal domain
phosphatase SSU72 (O42868) [more info...]
Chain information for Ssu72 AlphaFold.pdb #4
---
Chain | Description | UniProt
A | RNA polymerase II subunit A C-terminal domain phosphatase SSU72 |
SSU72_SCHPO
> select #3
2716 atoms, 2788 bonds, 341 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,46.452,0,1,0,118.49,0,0,1,170.65
> select #4
1588 atoms, 1620 bonds, 197 residues, 1 model selected
> view matrix models #4,1,0,0,35.115,0,1,0,95.863,0,0,1,128.74
> view matrix models #4,1,0,0,117.06,0,1,0,117.84,0,0,1,145.03
> view matrix models #4,1,0,0,119.2,0,1,0,96.31,0,0,1,113.25
> ui tool show "Fit in Map"
Fit molecule Pta1 1-322 fit.pdb (#2) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 2563 atoms
average map value = 0.9097, steps = 44
shifted from previous position = 0.00557
rotated from previous position = 0.0116 degrees
atoms outside contour = 683, contour level = 0.69429
Position of Pta1 1-322 fit.pdb (#2) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00012178 0.00016187 0.00242398
0.00012178 0.99999999 0.00001136 -0.01911983
-0.00016187 -0.00001134 0.99999999 0.02453735
Axis -0.05594818 0.79784257 0.60026414
Axis point 154.04285752 0.00000000 -14.72707952
Rotation angle (degrees) 0.01162420
Shift along axis -0.00066134
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 2716, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 46.45154304
0.00000000 1.00000000 0.00000000 118.48598351
0.00000000 0.00000000 1.00000000 170.64613052
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 170.64613052
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.04, steps = 80
shifted from previous position = 8.73
rotated from previous position = 11.3 degrees
atoms outside contour = 397, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.98524852 0.00959067 0.17086067 127.14985879
0.00670114 0.99550038 -0.09452029 96.76827111
-0.17099837 0.09427093 0.98075101 109.48053519
Axis 0.48341611 0.87535942 -0.00739889
Axis point 677.42271506 0.00000000 -274.41027841
Rotation angle (degrees) 11.26036901
Shift along axis 145.36327374
> select #3
2716 atoms, 2788 bonds, 341 residues, 1 model selected
> view matrix models #3,1,0,0,47.491,0,1,0,108.4,0,0,1,156.5
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 2716, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 47.49082002
0.00000000 1.00000000 0.00000000 108.40315773
0.00000000 0.00000000 1.00000000 156.49838494
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 156.49838494
> view matrix models #3,1,0,0,126.95,0,1,0,124.59,0,0,1,161.2
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 1.045, steps = 112
shifted from previous position = 5.44
rotated from previous position = 33.1 degrees
atoms outside contour = 498, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.88915610 0.43682172 -0.13633861 128.98703131
-0.36901918 0.86065197 0.35086041 122.89229012
0.27060355 -0.26165811 0.92644954 159.09327726
Axis -0.56145697 -0.37301812 -0.73866336
Axis point 83.73497643 29.01351484 0.00000000
Rotation angle (degrees) 33.05694959
Shift along axis -235.77809296
> ~select #3
Nothing selected
> ui tool show XMAS
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides.csv
Unique peptide pairs: 82 out of 82
Unique peptide pairs with pseudobonds: 21
Pseudobonds are stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_2,3,4.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_2,3,4.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides.csv
Unique peptide pairs: 199 out of 199
Unique peptide pairs with pseudobonds: 23
Pseudobonds are stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-
linked_peptides_2,3,4.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-
linked_peptides_2,3,4.tsv
> select #3
2716 atoms, 2788 bonds, 341 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.53545,0.49885,0.6815,127.96,-0.8259,-0.47799,-0.29903,124.58,0.17658,-0.72296,0.66794,159.72
> view matrix models
> #3,0.58229,-0.73611,0.34509,130.37,-0.52336,-0.66422,-0.53376,125.04,0.62212,0.1302,-0.77202,158.99
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 1.071, steps = 92
shifted from previous position = 3.14
rotated from previous position = 38 degrees
atoms outside contour = 424, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
-0.01256281 -0.95291610 0.30297373 129.27526752
-0.55613574 -0.24515114 -0.79411206 121.79982191
0.83099652 -0.17847079 -0.52687091 158.66438231
Axis 0.68183687 -0.58479739 0.43944339
Axis point 0.00000000 95.24068885 67.84668732
Rotation angle (degrees) 153.16274098
Shift along axis 86.64043868
> view matrix models
> #3,0.23389,-0.92921,-0.28611,129.47,-0.27375,0.21943,-0.93644,121.34,0.93293,0.29735,-0.20304,158.02
> view matrix models
> #3,0.2764,-0.88675,-0.37052,129.44,-0.24426,0.30806,-0.91948,121.23,0.92948,0.34465,-0.13144,157.94
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 1.05, steps = 84
shifted from previous position = 2.43
rotated from previous position = 17.8 degrees
atoms outside contour = 493, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.27061237 -0.73087265 -0.62657331 127.43780575
-0.25041823 0.57501011 -0.77888002 121.88249636
0.92954809 0.36767994 -0.02741899 159.79907265
Axis 0.57566312 -0.78129512 0.24122584
Axis point 17.61560935 0.00000000 167.55513598
Rotation angle (degrees) 95.21528502
Shift along axis 16.68271074
> ~select #6
2716 atoms, 2788 bonds, 20 pseudobonds, 341 residues, 2 models selected
> ~select #5
2716 atoms, 2788 bonds, 341 residues, 1 model selected
> select #4
1588 atoms, 1620 bonds, 11 pseudobonds, 197 residues, 3 models selected
> view matrix models
> #4,0.11669,-0.8427,0.52559,130.32,-0.88952,-0.32406,-0.32209,99.698,0.44175,-0.42994,-0.78741,106.36,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #4,0.15194,-0.56545,0.81067,130.32,-0.87484,-0.45863,-0.15593,100.34,0.45996,-0.68551,-0.56437,107.38,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #4,0.24532,-0.60315,0.75897,130.23,-0.83969,-0.52347,-0.14459,100.47,0.4845,-0.60183,-0.63487,107.03,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24532,-0.60315,0.75897,128.77,-0.83969,-0.52347,-0.14459,102.74,0.4845,-0.60183,-0.63487,108.81,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.105, steps = 96
shifted from previous position = 2.39
rotated from previous position = 54.1 degrees
atoms outside contour = 319, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.64923262 -0.06188542 0.75806807 127.55501409
-0.07800569 -0.99684642 -0.01457181 102.01418091
0.75657923 -0.04967313 -0.65201262 108.84479667
Axis -0.90807485 0.03851670 -0.41703301
Axis point -0.00000000 53.94240968 24.55749990
Rotation angle (degrees) 178.89255698
Shift along axis -157.29212384
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.105, steps = 40
shifted from previous position = 0.00897
rotated from previous position = 0.0573 degrees
atoms outside contour = 319, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.64951275 -0.06093976 0.75790470 127.54622346
-0.07736652 -0.99690645 -0.01385491 102.01860086
0.75640440 -0.04963751 -0.65221814 108.84081983
Axis -0.90815162 0.03807726 -0.41690617
Axis point 0.00000000 53.91779062 24.55819266
Rotation angle (degrees) 178.87115501
Shift along axis -157.32312971
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.105, steps = 44
shifted from previous position = 0.00933
rotated from previous position = 0.0226 degrees
atoms outside contour = 319, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.64940883 -0.06129364 0.75796521 127.55508496
-0.07750592 -0.99689063 -0.01420913 102.01547575
0.75647934 -0.04951926 -0.65214020 108.84381209
Axis -0.90812326 0.03821417 -0.41695542
Axis point 0.00000000 53.92300909 24.56088381
Rotation angle (degrees) 178.88602753
Shift along axis -157.32032084
> ~select #4
Nothing selected
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/DPS
> AlphaFold/rank_2_model_4_ptm_seed_0_unrelaxed.pdb" format pdb
Chain information for rank_2_model_4_ptm_seed_0_unrelaxed.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select #7
6093 atoms, 6246 bonds, 758 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.04299,-0.56496,0.824,-3.5104,-0.93821,0.26064,0.22765,-8.6041,-0.34338,-0.78287,-0.51884,-17.406
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.04299,-0.56496,0.824,193.17,-0.93821,0.26064,0.22765,53.678,-0.34338,-0.78287,-0.51884,128.64
> view matrix models
> #7,0.04299,-0.56496,0.824,229.42,-0.93821,0.26064,0.22765,81.471,-0.34338,-0.78287,-0.51884,105.57
> view matrix models
> #7,0.04299,-0.56496,0.824,216.88,-0.93821,0.26064,0.22765,83.094,-0.34338,-0.78287,-0.51884,79.107
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.64028,-0.36964,0.67336,220.29,-0.045075,-0.85702,-0.51331,61.873,0.76682,-0.35901,0.53207,87.972
> view matrix models
> #7,-0.96377,0.2637,0.04003,227.68,-0.2667,-0.9546,-0.13269,62.339,0.0032211,-0.13856,0.99035,94.395
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.96377,0.2637,0.04003,186.69,-0.2667,-0.9546,-0.13269,22.316,0.0032211,-0.13856,0.99035,146.84
> view matrix models
> #7,-0.96377,0.2637,0.04003,113.21,-0.2667,-0.9546,-0.13269,83.412,0.0032211,-0.13856,0.99035,144.95
> view matrix models
> #7,-0.96377,0.2637,0.04003,142.24,-0.2667,-0.9546,-0.13269,127.09,0.0032211,-0.13856,0.99035,180.33
Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#7) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 6093 atoms
average map value = 0.5064, steps = 196
shifted from previous position = 14.5
rotated from previous position = 37.9 degrees
atoms outside contour = 3814, contour level = 0.69429
Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#7) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
-0.83503496 0.43036282 -0.34278923 132.82750403
-0.17265422 -0.79652469 -0.57942984 116.68471205
-0.52240514 -0.42466017 0.73942992 174.25477849
Axis 0.23885884 0.27720451 -0.93064715
Axis point 101.64449744 70.31817397 0.00000000
Rotation angle (degrees) 161.09637531
Shift along axis -98.09716048
> ~select #7
Nothing selected
> hide #3 models
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides.csv
Unique peptide pairs: 82 out of 82
Unique peptide pairs with pseudobonds: 23
Pseudobonds are stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_2,4,7.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_2,4,7.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides.csv
Unique peptide pairs: 199 out of 199
Unique peptide pairs with pseudobonds: 29
Pseudobonds are stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-
linked_peptides_2,4,7.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-
linked_peptides_2,4,7.tsv
===== 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: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 16 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 72 days 2:09
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
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-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-XMAS: 1.1.1
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
et-xmlfile: 1.1.0
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openpyxl: 3.0.10
openvr: 1.16.801
packaging: 21.0
pandas: 1.4.2
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
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
seaborn: 0.11.2
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
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 , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash deleting some tool's interface |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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