![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15540 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-13.6.7-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x00007ff84f1a37c0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 266 in blob_list
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 256 in blob_values
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 206 in blob_sizes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 185 in triangle_values
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 166 in triangle_mask
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 40 in hide_surface_dust
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/dust.py", line 24 in hide_dust
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/surface/sop.py", line 335 in surface_dust
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 886 in hide_dust
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.mmcif.mmcif_write (total: 54)
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{
"uptime" : 140000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 505,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"coalitionID" : 1376,
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"build" : "22G720",
"releaseType" : "User"
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"captureTime" : "2024-07-02 04:33:16.2052 -0700",
"incident" : "26D7AEFF-0D95-4852-A668-1B1FFBAF4F8A",
"pid" : 27969,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-01 23:30:57.6979 -0700",
"procStartAbsTime" : 124507581857184,
"procExitAbsTime" : 142645857283456,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"93A775E5-7E73-5C5B-BA70-0DA69562D8DB","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "24312681-F021-0D25-6FCD-C32C28002F08",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 67125,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "19809CF3-0B70-4D14-9B52-87654B7EF0E9",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737488162647\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffd1000-7ffffffd2000 [ 4K] r-x\/r-x SM=SHM ",
"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":27969},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737488162647\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffd1000-7ffffffd2000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=5.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2528K 4 \nCG image 620K 39 \nColorSync 268K 30 \nCoreAnimation 652K 67 \nCoreGraphics 12K 2 \nCoreUI image data 5240K 39 \nFoundation 32K 2 \nKernel Alloc Once 8K 1 \nMALLOC 4.1G 753 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 108K 27 \nStack 156.7M 28 \nStack Guard 56.0M 1 \nVM_ALLOCATE 470.9M 348 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 49.4M 772 \n__DATA_CONST 53.6M 403 \n__DATA_DIRTY 1812K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 203.2M 148 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 953.2M 779 \ndyld private memory 420K 4 \nmapped file 253.0M 78 \nshared memory 3012K 33 \n=========== ======= ======= \nTOTAL 6.6G 3817 \nTOTAL, minus reserved VM space 6.3G 3817 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "e08ba2a96f39ceee9568a3ec2cb8edf69411901d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "645c2d2f9e69a025b0a37e29",
"factorPackIds" : {
},
"deploymentId" : 240000003
},
{
"rolloutId" : "6391cacc75b0720ff1f8c695",
"factorPackIds" : {
"COREOS_ICD" : "63957f508061fa721c8edc4a"
},
"deploymentId" : 240000007
}
],
"experiments" : [
{
"treatmentId" : "3dff9c91-a8fb-424e-a656-c8d6e6037574",
"experimentId" : "662152ede2d11d1408c4db33",
"deploymentId" : 400000010
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000003
}
]
}
}
===== 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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/T122P ADP/T122P ADP_after monomer
> fit_21Dec23.mrc" "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/T122P ADP/T122P ADP_NTD del_final
> aligned.pdb" "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/T122P
> ADP/cryosparc_P16_J178_006_volume_map.mrc"
Opened T122P ADP_after monomer fit_21Dec23.mrc as #1, grid size 400,400,400,
pixel 1, shown at level 0.136, step 2, values float32
Chain information for T122P ADP_NTD del_final aligned.pdb #2
---
Chain | Description
A B C D E F | No description available
Opened cryosparc_P16_J178_006_volume_map.mrc as #3, grid size 400,400,400,
pixel 1, shown at level 0.0293, step 2, values float32
> surface dust #1 size 10
> surface dust #3 size 10
> set bgColor white
> show atoms
> show cartoons
> hide atoms
> volume #3 step 1
> volume #1 step 1
> volume #1 level 0.2
> volume #3 level 0.2
> volume #3 level 0.1256
> volume #3 color #d4fb79
> transparency 70
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.1
> volume #3 level 0.2
> volume #3 level 0.15
> volume #3 level 0.1
> volume #3 level 0.12
> volume #3 level 0.2
> volume #3 level 0.13
> volume #3 level 0.15
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/T122P
> ADP/cryosparc_P16_J178_006_volume_map_half_A.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/T122P ADP/cryosparc_P16_J178_006_volume_map_half_B.mrc"
Opened cryosparc_P16_J178_006_volume_map_half_A.mrc as #4.1, grid size
400,400,400, pixel 1, shown at level 0.159, step 2, values float32
Opened cryosparc_P16_J178_006_volume_map_half_B.mrc as #4.2, grid size
400,400,400, pixel 1, shown at level 0.159, step 2, values float32
> volume #4.1 step 1
> volume #4.2 step 1
> surface dust #3 size 10
> surface dust #4.1 size 10
> surface dust #4.2 size 10
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4.2 models
> volume #4.1 level 0.2
> volume #4.1 level 0.4
> volume #4.1 level 0.3
> volume #4.1 level 0.25
> volume #4.1 level 0.1
> volume #4.1 level 0.2
> volume #4.2 level 0.2
> volume #4.1 level 0.15
> volume #4.1 level 0.2
> hide #!4.1 models
> show #!4.2 models
> close #1
> close #2
> close #3
> close #4
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/G128D
> ADP/cryosparc_P16_J94_008_volume_map_half_A.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G128D ADP/cryosparc_P16_J94_008_volume_map_half_B.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G128D ADP/cryosparc_P16_J94_008_volume_map.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G128D ADP/G128D ADP_final.cif"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G128D ADP/G128D ADP_monomer fit_21Dec23.mrc"
Summary of feedback from opening /Volumes/Subramaniam_Lab/Team_folder_2023/BC
Children's Collaboration/PDB Deposition Info/G128D ADP/G128D ADP_final.cif
---
warnings | Unknown polymer entity '1' near line 144
Missing or incomplete sequence information. Inferred polymer connectivity.
Opened cryosparc_P16_J94_008_volume_map_half_A.mrc as #1, grid size
400,400,400, pixel 1, shown at level 0.122, step 2, values float32
Opened cryosparc_P16_J94_008_volume_map_half_B.mrc as #2, grid size
400,400,400, pixel 1, shown at level 0.122, step 2, values float32
Opened cryosparc_P16_J94_008_volume_map.mrc as #3, grid size 400,400,400,
pixel 1, shown at level 0.023, step 2, values float32
Chain information for G128D ADP_final.cif #4
---
Chain | Description
A B C D E F | No description available
Opened G128D ADP_monomer fit_21Dec23.mrc as #5, grid size 400,400,400, pixel
1, shown at level 0.108, step 2, values float32
> show cartoons
> hide atoms
> surface dust #1 size 10
> surface dust #2 size 10
> surface dust #3 size 10
> surface dust #5 size 10
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> volume #3 level 0.15
> volume #5 step 1
> volume #5 level 0.15
> volume #1 level 0.15
> volume #2 level 0.15
> volume #3 level 0.25
> volume #5 level 0.2
> color #1 #8efa00ff models
> color #2 #ff9300ff models
> color #3 #d783ffff models
> transparency 70
> hide #!2 models
> hide #!1 models
> hide #!5 models
> volume #3 level 0.15
> hide #!3 models
> show #!5 models
> volume #5 level 0.25
> hide #!3 models
> show #!1 models
> volume #1 level 0.2
> show #!2 models
> hide #!1 models
> close #1
> close #2
> close #3
> close #4
> close #5
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/G156D ADP/G156D ADP_NTD del_final aligned.pdb"
Chain information for G156D ADP_NTD del_final aligned.pdb #1
---
Chain | Description
A B C D E F | No description available
> save "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/G156D ADP/G156D ADP_final.cif" relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close #1
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/G156D ATPgs/G156D ATPgS_NTD del_final aligned.pdb"
Chain information for G156D ATPgS_NTD del_final aligned.pdb #1
---
Chain | Description
A B C D E F | No description available
> save "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/G156D ATPgS/G156D ATPgS_final.cif"
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close #1
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/G156D
> ATPgS/cryosparc_P16_J112_006_volume_map.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G156D ATPgS/cryosparc_P16_J112_006_volume_map_half_B.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G156D ATPgS/cryosparc_P16_J112_006_volume_map_half_A.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G156D ATPgS/proper map_G156D ATPgs_4Jan24.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/PDB
> Deposition Info/G156D ATPgS/G156D ATPgS_final.cif"
Summary of feedback from opening /Volumes/Subramaniam_Lab/Team_folder_2023/BC
Children's Collaboration/PDB Deposition Info/G156D ATPgS/G156D ATPgS_final.cif
---
warnings | Unknown polymer entity '1' near line 160
Missing or incomplete sequence information. Inferred polymer connectivity.
Opened cryosparc_P16_J112_006_volume_map.mrc as #1, grid size 400,400,400,
pixel 1, shown at level 0.0277, step 2, values float32
Opened cryosparc_P16_J112_006_volume_map_half_B.mrc as #2, grid size
400,400,400, pixel 1, shown at level 0.131, step 2, values float32
Opened cryosparc_P16_J112_006_volume_map_half_A.mrc as #3, grid size
400,400,400, pixel 1, shown at level 0.13, step 2, values float32
Opened proper map_G156D ATPgs_4Jan24.mrc as #4, grid size 400,400,400, pixel
1, shown at level 0.162, step 2, values float32
Chain information for G156D ATPgS_final.cif #5
---
Chain | Description
A B C D E F | No description available
> surface dust #1 size 10
> surface dust #2 size 10
> surface dust #3 size 10
> surface dust #4 size 10
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> volume #4 step 1
> show cartoons
> hide atoms
> volume #1 level 0.15
> volume #2 level 0.2
> volume #4 level 0.25
> transparency 70
> color #1 #d783ffff models
> color #2 #ffd479ff models
> color #3 #00fa92ff models
> transparency 70
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> show #!4 models
> transparency #4 0
> lighting soft
> save /Users/sanaahmed/Desktop/image1.png supersample 3
> save /Users/sanaahmed/Desktop/image2.png supersample 3
> close #1
> close #2
> close #3
> close #4
> close #5
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/G156D ADP/G156D ADP zflip_monomer fit_21Dec23.mrc"
> "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's Collaboration/G156D
> ADP/G156D ADP_NTD del_final aligned.pdb"
Opened G156D ADP zflip_monomer fit_21Dec23.mrc as #1, grid size 400,400,400,
pixel 1, shown at level 0.142, step 2, values float32
Chain information for G156D ADP_NTD del_final aligned.pdb #2
---
Chain | Description
A B C D E F | No description available
> show cartoons
> hide atoms
> surface dust #1 size 10
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.25
> volume #1 step 1
> volume #1 level 0.26
> volume #1 level 0.25
> save /Users/sanaahmed/Desktop/image1.png supersample 3
> save /Users/sanaahmed/Desktop/image2.png supersample 3
> close #1
> close #2
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/R89Q ADP/R89Q ADP_after monomer fit_21Dec23.mrc"
Opened R89Q ADP_after monomer fit_21Dec23.mrc as #1, grid size 400,400,400,
pixel 1, shown at level 0.167, step 2, values float32
> volume #1 level 0.25
> volume #1 step 1
> surface dust #1 size 10
> volume #1 level 0.26
> volume #1 level 0.25
> save /Users/sanaahmed/Desktop/image1.png supersample 3
> save /Users/sanaahmed/Desktop/image2.png supersample 3
> open "/Volumes/Subramaniam_Lab/Team_folder_2023/BC Children's
> Collaboration/PDB Deposition Info/R89Q ADP/R89Q ADP_Unsharpened.mrc"
Opened R89Q ADP_Unsharpened.mrc as #2, grid size 400,400,400, pixel 1, shown
at level 0.0205, step 2, values float32
> volume #2 step 1
> surface dust #1 size 10
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 577.140.2~22
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 5 days, 12 hours, 22 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
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: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
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: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
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: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| 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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Hi Sana,
--Eric