![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15496 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00000001e5f1d300 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/serialize.py", line 70 in msgpack_deserialize
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 708 in restore
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 1004 in open
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 162 in _qt_safe
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.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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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "MacBookPro17,1",
"coalitionID" : 5493,
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"build" : "23A344",
"releaseType" : "User"
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"captureTime" : "2024-06-25 13:31:22.2199 -0600",
"codeSigningMonitor" : 1,
"incident" : "59496DD5-D8F7-4FB6-9C92-AC5254CDCC38",
"pid" : 23066,
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"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2024-06-21 14:28:03.9087 -0600",
"procStartAbsTime" : 9403222803235,
"procExitAbsTime" : 11925994994130,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "43CEB50D-8E40-87B1-DC8B-A0FC95EA9B4F",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "DF04C58C-40A3-4928-B688-8F4A9DD5CA51",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4338728791\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1029bc000-1029c0000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":23066},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4338728791\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1029bc000-1029c0000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_2/trimmed-8flj-
> AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
> renamed_real_space_refined_002.pdb
Chain information for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
G | No description available
H | No description available
> hbonds reveal true
1456 hydrogen bonds found
> select add #1
21746 atoms, 22179 bonds, 1456 pseudobonds, 1844 residues, 2 models selected
> style sel stick
Changed 21746 atom styles
> set bgColor white
> lighting soft
> select subtract #1
Nothing selected
> select /A
9364 atoms, 9562 bonds, 838 pseudobonds, 1076 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:592
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:592
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> /A:2-7,32-36,58-64,70-77,91-93,414-418,446-450,474-478,511-513,541-545,572-576,603-606,642-647,652-657,687-690,723-725,728-736,759-766,813-820,834-837,865-868,979-986,994-1000,1003-1006,1011-1013,1022-1024,1055-1058,1064-1067,1071-1074
1477 atoms, 1487 bonds, 94 pseudobonds, 150 residues, 2 models selected
> select /A:576
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:576-579
32 atoms, 31 bonds, 4 residues, 1 model selected
> select
> /A:2-7,32-36,58-64,70-77,91-93,414-418,446-450,474-478,511-513,541-545,572-576,603-606,642-647,652-657,687-690,723-725,728-736,759-766,813-820,834-837,865-868,979-986,994-1000,1003-1006,1011-1013,1022-1024,1055-1058,1064-1067,1071-1074
1477 atoms, 1487 bonds, 94 pseudobonds, 150 residues, 2 models selected
> select
> /A:10-22,38-52,79-82,109-122,125-128,130-137,149-161,167-175,183-187,208-219,231-236,243-246,253-260,267-269,271-286,290-298,301-320,349-364,367-373,381-384,390-412,426-437,457-467,484-496,500-502,524-527,531-538,546-548,550-552,562-568,578-580,583-585,587-598,612-631,660-679,699-720,740-753,772-785,793-797,800-808,822-824,842-851,872-875,899-902,905-909,914-917,929-938,953-956,960-963,966-970,1008-1010,1030-1041,1045-1052
4099 atoms, 4123 bonds, 343 pseudobonds, 475 residues, 2 models selected
> select /A
9364 atoms, 9562 bonds, 838 pseudobonds, 1076 residues, 2 models selected
> select /A
9364 atoms, 9562 bonds, 838 pseudobonds, 1076 residues, 2 models selected
> close session
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/supp.movies/3-model-
> comparison.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/supp.movies/3-model-
> comparison.cxs
Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size
324,324,324, pixel 1.1, shown at level 0.0681, step 1, values float32
Log from Thu Jun 6 16:35:37 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/whenriques/Downloads/3models+J1277-003-map_colored_sequences-
> corrected.cxs
Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size
324,324,324, pixel 1.1, shown at level 0.0681, step 1, values float32
Log from Wed Jun 5 14:28:52 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-
> sessions/3models+J1277-003-map_colored_sequences-corrected.cxs"
Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size
324,324,324, pixel 1.1, shown at level 0.0681, step 1, values float32
Log from Tue Jun 4 10:22:47 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/20240410-isolde-refinement-
> cas1-cdef-cas2H-cas3-GH-deleteG96HA2_real_space_refined_017.pdb"
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017.pdb #1
---
Chain | Description
A B C D | No description available
E F I J | No description available
G H | No description available
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/capture_jerry-modded.pdb"
Chain information for capture_jerry-modded.pdb #2
---
Chain | Description
A B | No description available
C D E F | No description available
> save "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/20240410-isolde-refinement-
> cas1-cdef-cas2H-cas3-GH-deleteG96HA2_real_space_refined_017_jerry-
> modded.pdb" models #2
> close
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/8flj-AFrepeat-dna-added-
> AFCas3-prelim-equilibration_real_space_refined_001-dna-bonds-added_Jerry-
> modded.pdb"
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb #1
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K L | No description available
M | No description available
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/capture_jerry-modded.pdb"
Chain information for capture_jerry-modded.pdb #2
---
Chain | Description
A B | No description available
C D E F | No description available
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/20240410-isolde-refinement-
> cas1-cdef-cas2H-cas3-GH-deleteG96HA2_real_space_refined_017_jerry-
> modded.pdb"
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb #3
---
Chain | Description
A B | No description available
C D E F | No description available
> open C:/Users/jarre/Downloads/cryosparc_P19_J1277_003_volume_map.mrc
Opened cryosparc_P19_J1277_003_volume_map.mrc as #4, grid size 324,324,324,
pixel 1.1, shown at level 0.0681, step 2, values float32
> vop flip #4
Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size
324,324,324, pixel 1.1, shown at step 1, values float32
> close #4
> set bgColor white
> graphics silhouettes true
> lighting shadows true
> lighting soft fillDirection -.1,.1,-.25 fillIntensity 0.1 direction -0, .1,
> -.2 intensity 0.2 multiShadow 128
> material specularReflectivity 0.1
> cartoon style protein xsection oval modeHelix default
> hide atoms
> show cartoons
> color #2/g,h #f69320ff
> color #1,2,3/a:1-94/b:1-94 #d799c4
> color #1,2,3/a:95-end/b:95-end #6d8fc9ff
> color #1,2,3/f,e #c2b59bff
> color #1,2,3/c,d #9c857a
> color #1/g:1-27/h:1-27 #f69320ff
> color #1/g:28-end/h:28-56 #92278f
> color #1/i/h:57-end #939598
> color #1/m,k #d91b5d
> color #1/l,j #a51e23
> hide #!5 models
> lighting simple
> hide #3 models
> hide #2 models
> save "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/3models+_colored_sequences-
> corrected .cxs" includeMaps true
——— End of log from Tue Jun 4 10:22:47 2024 ———
opened ChimeraX session
> split
Split 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb (#1)
into 13 models
Split capture_jerry-modded.pdb (#2) into 6 models
Split 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb (#3) into 6 models
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb G #1.7
---
Chain | Description
G | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb H #1.8
---
Chain | Description
H | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb I #1.9
---
Chain | Description
I | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb J #1.10
---
Chain | Description
J | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb K #1.11
---
Chain | Description
K | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb L #1.12
---
Chain | Description
L | No description available
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb M #1.13
---
Chain | Description
M | No description available
Chain information for capture_jerry-modded.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for capture_jerry-modded.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for capture_jerry-modded.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for capture_jerry-modded.pdb D #2.4
---
Chain | Description
D | No description available
Chain information for capture_jerry-modded.pdb E #2.5
---
Chain | Description
E | No description available
Chain information for capture_jerry-modded.pdb F #2.6
---
Chain | Description
F | No description available
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb F #3.6
---
Chain | Description
F | No description available
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #3.1 models
> show #3.2 models
> close
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/current-models/8flj-AFrepeat-
> dna-added-AFCas3-prelim-equilibration_real_space_refined_001-dna-bonds-
> added_Jerry-modded.pdb"
Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim-
equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb #1
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K L | No description available
M | No description available
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/current-models/prespacer-
> bound_jerry-modded.pdb"
prespacer-bound_jerry-modded.pdb title:
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]
Chain information for prespacer-bound_jerry-modded.pdb #2
---
Chain | Description | UniProt
A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB
1-1076
B | No description available |
C D E F | No description available |
G | No description available |
H | No description available |
> open "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-sessions/current-models/20240410-isolde-
> refinement-cas1-cdef-cas2H-cas3-GH-
> deleteG96HA2_real_space_refined_017_jerry-modded.pdb"
Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH-
deleteG96HA2_real_space_refined_017_jerry-modded.pdb #3
---
Chain | Description
A B | No description available
C D E F | No description available
> set bgColor white
> graphics silhouettes true
> lighting shadows true
> lighting soft fillDirection -.1,.1,-.25 fillIntensity 0.1 direction -0, .1,
> -.2 intensity 0.2 multiShadow 128
> material specularReflectivity 0.1
> cartoon style protein xsection oval modeHelix default
> hide atoms
> show cartoons
> color #2/g,h #f69320ff
> color #1,2,3/a:1-94/b:1-94 #d799c4
> color #1,2,3/a:95-end/b:95-end #6d8fc9ff
> color #1,2,3/f,e #c2b59bff
> color #1,2,3/c,d #9c857a
> color #1/g:1-27/h:1-27 #f69320ff
> color #1/g:28-end/h:28-56 #92278f
> color #1/i/h:57-end #939598
> color #1/m,k #d91b5d
> color #1/l,j #a51e23
> hide #2 models
> hide #3 models
> show #3 models
> show #2 models
> open C:/Users/jarre/Downloads/cryosparc_P19_J1277_003_volume_map.mrc
Opened cryosparc_P19_J1277_003_volume_map.mrc as #4, grid size 324,324,324,
pixel 1.1, shown at level 0.0681, step 2, values float32
> vop flip #4
Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size
324,324,324, pixel 1.1, shown at step 1, values float32
> close #4
> save "C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration
> complex/MyIntegrationMovie/Primary-
> sessions/3models+J1277-003-map_colored_sequences-corrected.cxs" includeMaps
> true
——— End of log from Wed Jun 5 14:28:52 2024 ———
opened ChimeraX session
> save /Users/whenriques/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/supp.movies/3-model-
> comparison.cxs includeMaps true
——— End of log from Thu Jun 6 16:35:37 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MJ123LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 17 days, 22 hours, 4 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
BenQ GW2760HS:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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