![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#7144 closed defect (can't reproduce)
Crash in garbage collection after tool destruction
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | 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
Thread 0x0000000317eec000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000002043a9600 (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 359 in _cleanup
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 396 in cb
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
{"app_name":"ChimeraX","timestamp":"2022-06-22 01:13:27.00 +0100","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"19101F0B-9FD2-4C60-B186-F224B2104829","name":"ChimeraX"}
{
"uptime" : 42000,
"procLaunch" : "2022-06-21 13:42:22.2615 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 20424255522,
"coalitionID" : 2046,
"osVersion" : {
"train" : "macOS 12.4",
"build" : "21F79",
"releaseType" : "User"
},
"captureTime" : "2022-06-22 01:13:14.4986 +0100",
"incident" : "19101F0B-9FD2-4C60-B186-F224B2104829",
"bug_type" : "309",
"pid" : 3581,
"procExitAbsTime" : 1015278027276,
"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",
"sip" : "enabled",
"vmRegionInfo" : "0x12928e78a888 is not in any region. Bytes after previous region: 19939628460169 Bytes before following region: 85132451469176\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x000092928e78a888","rawCodes":[1,161158153152648],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000092928e78a888 -> 0x000012928e78a888 (possible pointer authentication failure)"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x12928e78a888 is not in any region. Bytes after previous region: 19939628460169 Bytes before following region: 85132451469176\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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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/AlphaFold/Core
> Phosphatase module
> AlphaFold/prediction_Corepho_noDis2_4e8f1/rank_1_model_5_ptm_seed_0_unrelaxed.pdb"
Chain information for rank_1_model_5_ptm_seed_0_unrelaxed.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> /Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/cryosparc_P8_J39__localfilter.mrc
> format mrc
Opened cryosparc_P8_J39__localfilter.mrc as #2, grid size 128,128,128, pixel
1.96, shown at level 0.694, step 1, values float32
> select #1
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> set bgColor white
> lighting flat
> transparency 50
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.37758,0.46543,-0.8005,4.119,-0.85721,0.15123,0.49225,11.277,0.35017,0.87207,0.34188,-8.6283
> view matrix models
> #1,-0.82232,0.56199,0.089191,31.29,0.40101,0.68356,-0.60987,-22.91,-0.40371,-0.46574,-0.78747,-42.133
> view matrix models
> #1,-0.72483,0.58723,0.36024,36.672,0.6423,0.76512,0.045122,-9.7184,-0.24913,0.26409,-0.93177,-38.278
> view matrix models
> #1,0.082465,-0.25804,0.96261,30.218,0.64483,-0.72265,-0.24896,-35.035,0.75987,0.64125,0.1068,-21.927
> view matrix models
> #1,-0.020652,0.99118,-0.13087,21.759,0.99862,0.014117,-0.050661,-25.616,-0.048367,-0.13174,-0.9901,-46.997
> view matrix models
> #1,-0.42256,0.73376,-0.53202,14.203,0.70843,0.63353,0.31107,-6.0212,0.5653,-0.24545,-0.78752,-51.224
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.42256,0.73376,-0.53202,124.38,0.70843,0.63353,0.31107,110.22,0.5653,-0.24545,-0.78752,137.16
> view matrix models
> #1,-0.42256,0.73376,-0.53202,129.29,0.70843,0.63353,0.31107,130.9,0.5653,-0.24545,-0.78752,115.59
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.50313,0.75493,-0.42065,133.1,0.39525,0.63387,0.66482,142.89,0.76853,0.16823,-0.6173,122.18
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.50313,0.75493,-0.42065,128.94,0.39525,0.63387,0.66482,128.05,0.76853,0.16823,-0.6173,125.04
> ui tool show "Fit in Map"
Fit molecule rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) to map
cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms
average map value = 0.7995, steps = 168
shifted from previous position = 4.91
rotated from previous position = 35.5 degrees
atoms outside contour = 2942, contour level = 0.69429
Position of rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) relative to
cryosparc_P8_J39__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
-0.45678741 0.31007802 -0.83378468 122.16260201
0.11907689 0.95016139 0.28812156 127.79428353
0.88157017 0.03232581 -0.47094488 120.83486993
Axis -0.14660394 -0.98311951 -0.10946828
Axis point 20.65596258 0.00000000 82.86017704
Rotation angle (degrees) 119.26078393
Shift along axis -156.77415828
> ~select #1
Nothing selected
> ui tool show XMAS
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1).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
(1)_1.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_1.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports
2/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/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_1.pb
Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_1.tsv
> hide #!2 models
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Core
> Phosphatase module
> AlphaFold/prediction_Corepho_noDis2_4e8f1/rank_2_model_4_ptm_seed_0_unrelaxed.pdb"
Chain information for rank_2_model_4_ptm_seed_0_unrelaxed.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Core
> Phosphatase module
> AlphaFold/prediction_Corepho_noDis2_4e8f1/rank_3_model_1_ptm_seed_0_unrelaxed.pdb"
Chain information for rank_3_model_1_ptm_seed_0_unrelaxed.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select #5
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> view matrix models #5,1,0,0,71.167,0,1,0,47.419,0,0,1,45.429
> view matrix models #5,1,0,0,70.208,0,1,0,41.442,0,0,1,41.021
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.44006,0.89781,-0.016977,42.505,-0.08176,-0.021232,0.99643,34.153,0.89424,0.43987,0.082748,63.541
> view matrix models
> #5,-0.34896,-0.16145,0.92312,38.86,0.87933,0.28421,0.38211,55.73,-0.32405,0.94507,0.042791,40.856
> select #6
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> view matrix models
> #6,0.37493,-0.54152,-0.75245,-1.0825,-0.50119,0.56441,-0.65593,-1.2934,0.77989,0.62305,-0.059795,-14.815
> view matrix models
> #6,-0.60334,-0.19311,-0.77375,0.029629,0.79748,-0.14163,-0.58649,-1.0629,0.0036656,-0.9709,0.23945,-0.82265
> view matrix models
> #6,0.51444,0.024965,-0.85716,-5.5897,0.74871,-0.5004,0.43478,9.5256,-0.41806,-0.86544,-0.27612,-4.2627
> show #!2 models
> select #2
2 models selected
> view matrix models
> #2,0.99775,0.054774,0.038582,-11.466,-0.054425,0.99847,-0.010043,8.2415,-0.039073,0.0079208,0.9992,3.9746
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99775,0.054774,0.038582,-171.73,-0.054425,0.99847,-0.010043,-75.754,-0.039073,0.0079208,0.9992,-82.121
> view matrix models
> #2,0.99775,0.054774,0.038582,-148.26,-0.054425,0.99847,-0.010043,-81.649,-0.039073,0.0079208,0.9992,-82.453
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.62928,-0.22646,0.74346,-159.83,0.51183,0.84062,-0.17717,-110.71,-0.58484,0.49201,0.64489,-28.09
> view matrix models
> #2,0.76388,-0.082181,0.64011,-180.77,-0.10647,0.96222,0.25059,-104.68,-0.63652,-0.25957,0.72627,59.955
> view matrix models
> #2,0.15848,-0.89213,0.42306,21.921,0.79621,0.36886,0.47958,-173.56,-0.5839,0.26084,0.76878,-15.965
> view matrix models
> #2,0.30176,-0.90058,0.31287,19.542,0.78959,0.41999,0.44738,-174.82,-0.53431,0.11204,0.83783,-12.84
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.30176,-0.90058,0.31287,58.072,0.78959,0.41999,0.44738,-166.69,-0.53431,0.11204,0.83783,20.73
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.36653,-0.82692,0.42645,117.08,0.83752,-0.093608,0.53833,-121.44,-0.40524,0.55447,0.72687,-35.119
> view matrix models
> #2,-0.12308,-0.6628,0.73861,26.13,0.98558,0.0054789,0.16915,-103.9,-0.11616,0.74878,0.65256,-85.124
> view matrix models
> #2,0.32552,-0.6707,0.66648,-19.115,0.83717,0.5321,0.12658,-144.59,-0.43953,0.51676,0.7347,-27.259
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.32552,-0.6707,0.66648,-11.332,0.83717,0.5321,0.12658,-151.28,-0.43953,0.51676,0.7347,-27.116
> view matrix models
> #2,0.32552,-0.6707,0.66648,-9.4136,0.83717,0.5321,0.12658,-137.85,-0.43953,0.51676,0.7347,-51.884
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.089513,-0.31791,0.94389,-37.373,0.78269,0.56362,0.26406,-152.87,-0.61594,0.76241,0.19838,9.6486
> view matrix models
> #2,0.41365,-0.76093,0.49987,12.423,0.84267,0.52786,0.10621,-135.36,-0.34468,0.37729,0.85956,-62.78
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.41365,-0.76093,0.49987,24.148,0.84267,0.52786,0.10621,-130.34,-0.34468,0.37729,0.85956,-68.072
Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#5) to map
cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms
average map value = 0.8322, steps = 100
shifted from previous position = 1.89
rotated from previous position = 15.5 degrees
atoms outside contour = 2748, contour level = 0.69429
Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#5) relative to
cryosparc_P8_J39__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.82201767 -0.20147306 0.53263080 125.63556203
0.46769559 0.77246050 -0.42961100 126.13520323
-0.32488121 0.60225691 0.72920424 119.56900014
Axis 0.68823856 0.57194611 0.44632425
Axis point 0.00000000 -29.33241355 26.93239860
Rotation angle (degrees) 48.55955516
Shift along axis 211.97632088
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1).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
(1)_5.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_5.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports
2/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/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_5.pb
Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_5.tsv
> close #5
> close #8
> close #3
> ~select #7
2 models selected
> select #7
Nothing selected
> close #7
> close #4
> select #6
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.51444,0.024965,-0.85716,26.579,0.74871,-0.5004,0.43478,19.42,-0.41806,-0.86544,-0.27612,43.459
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.87076,-0.089912,-0.48342,29.121,0.13913,-0.89791,0.41762,23.533,-0.47161,-0.43091,-0.76935,37.133
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.87076,-0.089912,-0.48342,31.095,0.13913,-0.89791,0.41762,27.975,-0.47161,-0.43091,-0.76935,50.135
> view matrix models
> #6,0.87076,-0.089912,-0.48342,31.608,0.13913,-0.89791,0.41762,45.423,-0.47161,-0.43091,-0.76935,30.883
> view matrix models
> #6,0.87076,-0.089912,-0.48342,34.829,0.13913,-0.89791,0.41762,48.51,-0.47161,-0.43091,-0.76935,40.021
Fit molecule rank_3_model_1_ptm_seed_0_unrelaxed.pdb (#6) to map
cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms
average map value = 0.8079, steps = 84
shifted from previous position = 6.24
rotated from previous position = 9.83 degrees
atoms outside contour = 2895, contour level = 0.69429
Position of rank_3_model_1_ptm_seed_0_unrelaxed.pdb (#6) relative to
cryosparc_P8_J39__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.73818032 -0.51605516 0.43448463 123.70794997
-0.67169057 -0.62203891 0.40236722 126.53414362
0.06262267 -0.58885879 -0.80580626 120.07375117
Axis -0.92632576 0.34751441 -0.14544523
Axis point 0.00000000 103.26273783 25.72532531
Rotation angle (degrees) 147.65398602
Shift along axis -88.08557767
> open
> /Users/alexau/Downloads/prediction_168S_a5f72/rank_1_model_4_ptm_seed_0_unrelaxed.pdb
Chain information for rank_1_model_4_ptm_seed_0_unrelaxed.pdb #3
---
Chain | Description
A | No description available
B | No description available
> select #3
2944 atoms, 3024 bonds, 368 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> ~select #3
Nothing selected
> ui tool show Matchmaker
> hide #3 models
> show #3 models
> hide #6 models
> show #6 models
> select #6/A:1-197
1587 atoms, 1619 bonds, 197 residues, 1 model selected
> select #6/B:1-322
2563 atoms, 2608 bonds, 322 residues, 1 model selected
> select #6/C:1-91
741 atoms, 758 bonds, 91 residues, 1 model selected
> select #6/D:1-341
2715 atoms, 2787 bonds, 341 residues, 1 model selected
> ui tool show Matchmaker
> select #5/D:1-341
Nothing selected
> select #5/D:1-341
Nothing selected
> select #5/D:1-341
Nothing selected
> select #5/D:1-341
Nothing selected
> select #5/D:1-341
Nothing selected
> select #5/C:1-91
Nothing selected
> select #3
2944 atoms, 3024 bonds, 368 residues, 1 model selected
> ~select #3
Nothing selected
> select #6
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> select #6/D:1-341
2715 atoms, 2787 bonds, 341 residues, 1 model selected
> select #6/D:1-341
2715 atoms, 2787 bonds, 341 residues, 1 model selected
> select #6/C:1-91
741 atoms, 758 bonds, 91 residues, 1 model selected
> select #6/D:1-341
2715 atoms, 2787 bonds, 341 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #6 to #1/D pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rank_1_model_5_ptm_seed_0_unrelaxed.pdb, chain D (#1) with
rank_3_model_1_ptm_seed_0_unrelaxed.pdb, chain D (#6), sequence alignment
score = 1720.7
RMSD between 328 pruned atom pairs is 0.552 angstroms; (across all 341 pairs:
1.063)
> select #3
2944 atoms, 3024 bonds, 368 residues, 1 model selected
> select #6
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> view matrix models
> #6,0.85616,0.50727,0.09826,92.404,0.20426,-0.50695,0.83742,121.13,0.47462,-0.6969,-0.53765,39.803
> view matrix models
> #6,0.85616,0.50727,0.09826,93.248,0.20426,-0.50695,0.83742,100.98,0.47462,-0.6969,-0.53765,45.059
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.6912,0.49542,-0.52612,88.719,0.72164,-0.43435,0.53905,96.399,0.03854,-0.75226,-0.65774,45.827
> view matrix models
> #6,0.79839,0.4352,-0.41615,89.607,0.6016,-0.6061,0.52032,97.608,-0.025783,-0.66577,-0.74571,44.83
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.79839,0.4352,-0.41615,71.768,0.6016,-0.6061,0.52032,52.554,-0.025783,-0.66577,-0.74571,14.566
> view matrix models
> #6,0.79839,0.4352,-0.41615,31.472,0.6016,-0.6061,0.52032,64.803,-0.025783,-0.66577,-0.74571,26.842
> view matrix models
> #6,0.79839,0.4352,-0.41615,35.177,0.6016,-0.6061,0.52032,54.367,-0.025783,-0.66577,-0.74571,42.539
> view matrix models
> #6,0.79839,0.4352,-0.41615,35.588,0.6016,-0.6061,0.52032,57.327,-0.025783,-0.66577,-0.74571,40.914
> close #6
> select #1
7606 atoms, 7772 bonds, 951 residues, 1 model selected
> view matrix models
> #1,-0.45679,0.31008,-0.83378,27.6,0.11908,0.95016,0.28812,60.243,0.88157,0.032326,-0.47094,37.636
> view matrix models
> #1,-0.45679,0.31008,-0.83378,38.377,0.11908,0.95016,0.28812,57.079,0.88157,0.032326,-0.47094,48.839
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.045432,0.046119,-0.9979,25.175,-0.20687,0.97771,0.035768,55.574,0.97731,0.20481,0.05396,61.934
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.045432,0.046119,-0.9979,30.697,-0.20687,0.97771,0.035768,45.854,0.97731,0.20481,0.05396,51.462
> view matrix models
> #1,0.045432,0.046119,-0.9979,26.235,-0.20687,0.97771,0.035768,49.314,0.97731,0.20481,0.05396,51.127
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.17175,0.33372,-0.92689,34.1,-0.16651,0.9175,0.36119,55.586,0.97097,0.21637,-0.10201,47.747
Fit molecule rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) to map
cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms
average map value = 0.7995, steps = 236
shifted from previous position = 10.6
rotated from previous position = 58.7 degrees
atoms outside contour = 2943, contour level = 0.69429
Position of rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) relative to
cryosparc_P8_J39__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
-0.45683527 0.31006471 -0.83376341 122.16744111
0.11906275 0.95016487 0.28811595 127.78866813
0.88154728 0.03235136 -0.47098597 120.83841766
Axis -0.14659011 -0.98312119 -0.10947176
Axis point 20.66043040 0.00000000 82.86266713
Rotation angle (degrees) 119.26359055
Shift along axis -156.76868015
> select #3
2944 atoms, 3024 bonds, 368 residues, 1 model selected
> matchmaker #3 to #1/D pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rank_1_model_5_ptm_seed_0_unrelaxed.pdb, chain D (#1) with
rank_1_model_4_ptm_seed_0_unrelaxed.pdb, chain B (#3), sequence alignment
score = 1748.3
RMSD between 324 pruned atom pairs is 0.419 angstroms; (across all 341 pairs:
2.281)
> ~select #3
Nothing selected
> ui tool show XMAS
Traceback (most recent call last):
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 285, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 285, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports
2/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/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_1,3.pb
Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_1,3.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1).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
(1)_1,3.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_1,3.tsv
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #1 models
> close #1
> close #3
> close #4
> close #5
> open
> /Users/alexau/Downloads/prediction_CorePho_noDis2_534_591_ba56f/rank_1_model_5_ptm_seed_0_unrelaxed.pdb
Chain information for rank_1_model_5_ptm_seed_0_unrelaxed.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select #1
7232 atoms, 7393 bonds, 903 residues, 1 model selected
> view matrix models
> #1,-0.05011,-0.20274,0.97795,24.294,0.92547,0.35872,0.12179,-7.3458,-0.3755,0.91116,0.16966,-8.1856
> view matrix models
> #1,-0.85842,-0.27988,0.42987,20.449,0.24265,-0.9599,-0.14042,-11.985,0.45194,-0.016235,0.8919,-5.3662
> view matrix models
> #1,-0.76636,-0.35685,0.53419,21.287,0.5516,-0.79175,0.26244,-6.5736,0.32929,0.49578,0.8036,-3.9849
> view matrix models
> #1,-0.53048,0.84178,0.099935,16.584,0.37137,0.12481,0.92006,9.934,0.76202,0.52519,-0.37882,-27.903
> view matrix models
> #1,-0.37804,-0.11556,-0.91855,-6.2144,0.32181,0.91391,-0.24742,-7.1082,0.86806,-0.38913,-0.30831,-31.05
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.37804,-0.11556,-0.91855,24.752,0.32181,0.91391,-0.24742,31.051,0.86806,-0.38913,-0.30831,52.773
> view matrix models
> #1,-0.37804,-0.11556,-0.91855,37.423,0.32181,0.91391,-0.24742,58.451,0.86806,-0.38913,-0.30831,45.128
Fit molecule rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) to map
cryosparc_P8_J39__localfilter.mrc (#2) using 7232 atoms
average map value = 0.8516, steps = 124
shifted from previous position = 6.62
rotated from previous position = 27 degrees
atoms outside contour = 2502, contour level = 0.69429
Position of rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) relative to
cryosparc_P8_J39__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
-0.04175649 0.93328165 -0.35670965 124.64432532
0.49389743 0.32963059 0.80461731 128.65548557
0.86851697 -0.14257999 -0.47470962 122.03972416
Axis -0.58839832 -0.76110995 -0.27294518
Axis point -9.37721050 0.00000000 39.36952496
Rotation angle (degrees) 126.39991928
Shift along axis -204.57163495
> ~select #1
Nothing selected
> select #1
7232 atoms, 7393 bonds, 903 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> ~select #1
Nothing selected
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports
2/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: 22
Pseudobonds are stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_1.pb
Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_1.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1).csv
Unique peptide pairs: 199 out of 199
Unique peptide pairs with pseudobonds: 24
Pseudobonds are stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_1.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_1.tsv
> open
> /Users/alexau/Downloads/prediction_CorePhoDis273_5477c/rank_1_model_4_ptm_seed_0_unrelaxed.pdb
Chain information for rank_1_model_4_ptm_seed_0_unrelaxed.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide atoms
> show cartoons
> select #5
10132 atoms, 10361 bonds, 1262 residues, 1 model selected
> view matrix models #5,1,0,0,-14.923,0,1,0,-5.8194,0,0,1,-33.546
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.6273,-0.52263,-0.57737,-22.974,0.76261,0.26193,0.59146,-6.6003,-0.15789,-0.81133,0.56287,-42.588
> view matrix models
> #5,0.42451,-0.40902,-0.80777,-23.651,0.25601,-0.80152,0.5404,-19.148,-0.86847,-0.4362,-0.23554,-45.147
> view matrix models
> #5,-0.12668,-0.84696,-0.51635,-30.205,-0.98617,0.051451,0.15754,-19.765,-0.10687,0.52917,-0.84176,-33.321
> view matrix models
> #5,-0.14285,-0.76392,-0.6293,-29.799,-0.9887,0.080905,0.12622,-19.584,-0.045512,0.64022,-0.76684,-31.815
> view matrix models
> #5,-0.040568,0.017318,-0.99903,-23.033,-0.94318,0.32935,0.04401,-17.281,0.32979,0.94405,0.0029733,-25.289
> view matrix models
> #5,0.15561,0.49048,-0.85745,-17.377,-0.87908,0.46469,0.10627,-15.57,0.45057,0.73722,0.50348,-25.364
> view matrix models
> #5,0.53123,0.83822,-0.12321,-10.533,-0.76895,0.53807,0.34524,-13.768,0.35568,-0.088661,0.93039,-32.363
> ~select #5
Nothing selected
> select #5
10132 atoms, 10361 bonds, 1262 residues, 1 model selected
> view matrix models
> #5,-0.078884,0.91689,0.39127,-12.392,0.41789,-0.32593,0.84802,-13.328,0.90507,0.2304,-0.35745,-28.947
> view matrix models
> #5,-0.073012,0.75796,0.6482,-13.232,0.89878,-0.23169,0.37216,-10.624,0.43227,0.60977,-0.66433,-29.032
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.073012,0.75796,0.6482,44.058,0.89878,-0.23169,0.37216,9.228,0.43227,0.60977,-0.66433,35.452
> hide #1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.0049357,0.59634,-0.80271,40.07,-0.2598,0.77593,0.57484,11.698,0.96565,0.20571,0.15876,36.752
> view matrix models
> #5,-0.48781,0.37102,-0.79018,35.169,-0.11081,0.87154,0.47764,13.229,0.86589,0.32056,-0.38404,36.048
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.48781,0.37102,-0.79018,43.508,-0.11081,0.87154,0.47764,52.296,0.86589,0.32056,-0.38404,42.362
> view matrix models
> #5,-0.48781,0.37102,-0.79018,49.92,-0.11081,0.87154,0.47764,50.091,0.86589,0.32056,-0.38404,38.328
Fit molecule rank_1_model_4_ptm_seed_0_unrelaxed.pdb (#5) to map
cryosparc_P8_J39__localfilter.mrc (#2) using 10132 atoms
average map value = 0.582, steps = 196
shifted from previous position = 13.5
rotated from previous position = 34.6 degrees
atoms outside contour = 5524, contour level = 0.69429
Position of rank_1_model_4_ptm_seed_0_unrelaxed.pdb (#5) relative to
cryosparc_P8_J39__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
-0.18847903 0.97826567 0.08644046 114.93170075
0.44182459 0.00585777 0.89708235 121.16459042
0.87707851 0.20727272 -0.43332589 124.29387326
Axis -0.58535955 -0.67092066 -0.45521387
Axis point -2.89716252 0.00000000 19.79061174
Rotation angle (degrees) 143.89841341
Shift along axis -205.14849042
> ~select #5
Nothing selected
> show #1 models
> hide #5 models
Please select pseudobonds
> ~select #4
21 pseudobonds, 1 model selected
> ~select #3
Nothing selected
/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py:1100: UserWarning: Tight layout not applied.
The left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
> close #5
> select /A
2452 atoms, 2496 bonds, 16 pseudobonds, 307 residues, 3 models selected
> color (#1 & sel) lime
> select /B
1587 atoms, 1619 bonds, 11 pseudobonds, 197 residues, 3 models selected
> color (#1 & sel) blue
> select /C
2715 atoms, 2787 bonds, 341 residues, 1 model selected
> color sel magenta
> select /D
478 atoms, 491 bonds, 58 residues, 1 model selected
> color sel cyan
> select #1
7232 atoms, 7393 bonds, 43 pseudobonds, 903 residues, 3 models selected
> ~select #1
Nothing selected
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> ui tool show XMAS
> ~select #3
22 pseudobonds, 1 model selected
> ~select #4
Nothing selected
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> save /Users/alexau/Desktop/image2.png supersample 3
> hide #!2 models
> show #!2 models
> hide #!2 models
> select /A
2452 atoms, 2496 bonds, 16 pseudobonds, 307 residues, 3 models selected
> color (#1 & sel) lime
> select /B
1587 atoms, 1619 bonds, 11 pseudobonds, 197 residues, 3 models selected
> color (#1 & sel) blue
> select clear
> show #!2 models
> save /Users/alexau/Desktop/image3.png supersample 3
> hide #!2 models
> save /Users/alexau/Desktop/image4.png supersample 3
> show #!2 models
> hide #!2 models
> show #!2 models
> save /Users/alexau/Desktop/image5.png supersample 3
> hide #!2 models
> save /Users/alexau/Desktop/image6.png supersample 3
> open /Users/alexau/Downloads/AF-P23193-F1-model_v2.pdb
AF-P23193-F1-model_v2.pdb title:
Alphafold monomer V2.0 prediction for transcription elongation factor A
protein 1 (P23193) [more info...]
Chain information for AF-P23193-F1-model_v2.pdb #5
---
Chain | Description | UniProt
A | transcription elongation factor A protein 1 | TCEA1_HUMAN
> hide #4 models
> hide #3 models
> hide #1 models
> ui tool show "Side View"
> view #5 clip false
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Ppn1
> AlphaFold/ppn1_ffb23_unrelaxed_rank_1_model_3.pdb"
Chain information for ppn1_ffb23_unrelaxed_rank_1_model_3.pdb #6
---
Chain | Description
A | No description available
> hide #5 models
> color #6 #a6a6a6 transparency 0
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
===== 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 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 11:47
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 (14)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → UI |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection after tool destruction |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 3 years ago
I suspect many or most of our crashes are PyQt reference counting bugs, where PyQt decrements a reference count but in fact the Python object is still accessible. We see lots of crashes in c_function() where Python is calling to a C implemented routine that then crashes -- I suspect those are calls to methods of deleted PyQt widgets.
At any rate our UI.remove_tool() code that runs garbage collection after a timer has a comment
# get garbage collection to break callback loops in deleted tools
# that might be triggered by live tools (e.g. settings changes)
# particularly since WA_DeleteOnClose can nuke the Qt side
that I don't understand. How could garbage collection prevent a callback?
comment:4 by , 3 years ago
Tools will frequently update their UI based on triggers coming from settings changes. If the Python side of the tool isn't properly garbage collected, that trigger callback will still be active when that setting is changed from another source (frequently a second, live, instance of the same tool), and will try to update a UI widget whose C++ side is dead.
follow-up: 5 comment:5 by , 3 years ago
How could a tool be garbage collected if there is a settings changed callback registered that calls that tool? When the tool is deleted it has to remove the settings changed callback or it will never get garbage collected. If you are talking about the scenario where the Python of a tool does not realize that its Qt widgets have been deleted (e.g. delete on close) it seems like there are two solutions. 1) The Python should in fact get notified before the Qt widgets are deleted (e.g. get a Qt close event, or 2) the tool accounts for the fact that its Qt widgets might have been deleted as tests in any code paths that don't come from those Qt widgets. Option 2 is a bit of a nightmare, so option 1 is preferred. If garbage collection is somehow an option 3, I don't understand it.
comment:6 by , 3 years ago
Option objects can be handed a settings object and an attribute name and the Option itself handles responding to settings changes, updating the settings if the Option UI element is changed, and calling back to the parent UI if appropriate. The settings object stops listening to the settings trigger in its del method. The parent UI doesn't manually handle the cleanup of all it Option objects. So running a full garbage collection will break reference loops in the parent UI and get everything properly garbage collected.
follow-up: 8 comment:8 by , 3 years ago
I am not sure my understanding of Python garbage collection limitations is current. Back in the day if a reference cycle involved any methods of instances with __del__ methods then they would not be garbage collected because Python did not know which order to execute the __del__ methods. Also I think the __del__ methods could add references to that bring the garbage back to life. But those problems were handled by PEP 442 in 2013, Python 3.4 https://peps.python.org/pep-0442/ So I am not sure where "cycle breaking" is currently needed in Python to assist garbage collection. Sounds like the aim of the garbage collection is to get the Settings instance __del__() called so it does not end up calling the Option, and the reason it might call is because a weakref exists so it is accessible even though garbage collection would remove it. That is really convoluted. I wish we could avoid code like that which wastes so much time trying to understand it. In general, relying on the timing of when a __del__() method is called is disasterous. But I guess this design is because the Option does not get any explicit clean up by its parent. It seems like a cleaner solution would be that the Option code itself blocks the setting callback if the Qt widget is deleted. If the Option isn't going to have explicit cleanup then it should be responsible for handling callbacks coming to a dead Option.
comment:9 by , 3 years ago
The situation isn't as complicated as you are making it out to be. There is one strong reference to the Option coming from the parent UI. There are strong reference cycles to other objects _within_ the parent UI that aren't being broken by the "cheap" garbage collection that Python does frequently (it does full garbage collection significantly less often). Breaking the cycles within the parent UI allows the Option reference to go away.
follow-up: 10 comment:10 by , 3 years ago
Ok. I didn't even know Python has different types of garbage collection ("cheap" vs "full"). I try for explicit cleanup in all Python code. Relying on the timing of __del__() or that it is ever called causes too many problems. Same with Qt which likes to use "deleteLater()" for all its cleanup. Best to make sure things work even if Qt objects that are gone never get deleted. Whenever I see the removeDockWidget() crash I get the unpleasant feeling that this is a Qt bug caused by misjudging when deleteLater() actually did its work.
comment:11 by , 3 years ago
I see your point of view, but in this case if the Option isn't destroyed as part of the garbage collection then that is a memory leak and a bug in its own right that I would like to know about -- and will because of the resulting callback-to-dead-object behavior.
follow-up: 12 comment:12 by , 3 years ago
Of course memory leaks can be trouble. But the code that puts in a 100 millisecond timer and relies on that to avoid a callback to a dead Option can create nightmarish debugging situations because the bug only hits if the irreproducible timing is just right.
comment:13 by , 3 years ago
These are user interface settings and change upon user interaction (usually with another copy of the same tool) and are therefore highly unlikely to change within .1 second of tool destruction. I can envision some scenarios where your concern might come into play, but they seem pretty unlikely. At least, a lot less likely than uncovering a memory leak.
comment:14 by , 3 years ago
There was a failure starting the XMAS tool earlier in this log that I can possibly envision causing a crash during garbage collection.
Note:
See TracTickets
for help on using tickets.
I understand _what's_ happening (garbage collection is being called to break callback loops and actually dispose of a closed tool), but I don't understand _why_ that causes a crash.