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Opened 14 months ago
Closed 14 months ago
#15771 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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
Thread 0x00007000055c5000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff8505da7c0 (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/OpenGL/arrays/lists.py", line 157 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 791 in draw_self
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1560 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1289 in draw_transparent
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559 in draw_transparent
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 265 in _draw_scene
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_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.pdb_lib._load_libs, 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.surface._surface, 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.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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{
"uptime" : 750000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac18,3",
"coalitionID" : 1069,
"osVersion" : {
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"build" : "22G720",
"releaseType" : "User"
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"captureTime" : "2024-08-15 16:57:54.3120 -0500",
"incident" : "ACDD58CE-CB47-45F6-B895-55539015AE97",
"pid" : 27052,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-13 15:09:30.8056 -0500",
"procStartAbsTime" : 629857529050907,
"procExitAbsTime" : 754982273011471,
"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":"3387C9E5-741D-523D-8075-5DCC94101667","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "77CFA7F5-DC7C-4870-3C7A-6662DF07730E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 24899,
"sleepWakeUUID" : "7F8645AA-AB1C-419E-B737-43A0E56906AB",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737486364503\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe1a000-7fffffe1b000 [ 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":27052},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737486364503\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe1a000-7fffffe1b000 [ 4K] r-x\/r-x SM=SHM ",
"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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"size" : 16814080,
"uuid" : "0de06622-e926-3354-8b51-b64f04f21173",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.77.138"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703342120960,
"size" : 624112,
"uuid" : "2faf54fd-58e6-360c-9bd8-2fbfe8be93d3",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
}
],
"sharedCache" : {
"base" : 140703341498368,
"size" : 21474836480,
"uuid" : "5b024447-21cb-39dc-9946-0924a6000a4b"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 6720K 8 \nCG image 632K 43 \nColorSync 264K 30 \nCoreAnimation 620K 70 \nCoreGraphics 24K 4 \nCoreUI image data 5308K 37 \nFoundation 32K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.3G 751 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 104K 26 \nStack 171.7M 27 \nStack Guard 56.0M 1 \nVM_ALLOCATE 275.8M 261 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 48.2M 751 \n__DATA_CONST 51.0M 387 \n__DATA_DIRTY 1795K 224 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 203.2M 151 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 920.3M 757 \ndyld private memory 420K 4 \nmapped file 243.3M 64 \nshared memory 3004K 30 \n=========== ======= ======= \nTOTAL 3.6G 3656 \nTOTAL, minus reserved VM space 3.4G 3656 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "11033a2ccf60086416fd3980e2e1141670601cfe",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
},
{
"rolloutId" : "6425c75e4327780c10cc4252",
"factorPackIds" : {
"SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE" : "642600a457e7664b1698eb32"
},
"deploymentId" : 240000004
}
],
"experiments" : [
{
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"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
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 "/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/Combine 3
> components/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_001.pdb"
Chain information for combine_3comp_W19-coot-8_real_space_refined_093_001.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> lighting simple
> hide atoms
> show cartoons
> select /H
2030 atoms, 2085 bonds, 1 pseudobond, 251 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /L
846 atoms, 867 bonds, 1 pseudobond, 107 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/Combine 3
> components/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_001.pdb"
Chain information for combine_3comp_W19-coot-8_real_space_refined_093_001.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> close #2
> open /Users/boskostojanovski/Desktop/ALL-coot-5.pdb
Chain information for ALL-coot-5.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select #2/A
10700 atoms, 10992 bonds, 1 pseudobond, 1318 residues, 2 models selected
> select #2/C
1863 atoms, 1905 bonds, 235 residues, 1 model selected
> select #2/B
1089 atoms, 1114 bonds, 139 residues, 1 model selected
> select #2/D
4496 atoms, 4615 bonds, 1 pseudobond, 565 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select add #2
13652 atoms, 14012 bonds, 1 pseudobond, 1692 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #1
13272 atoms, 13621 bonds, 3 pseudobonds, 1650 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.82041,0.57151,0.017232,-69.406,0.46299,-0.64634,-0.60654,298.32,-0.33551,0.50559,-0.79487,258.38
> view matrix models
> #1,0.57932,0.58435,0.56826,-120.8,0.81261,-0.46848,-0.34668,169.65,0.063638,0.66261,-0.74625,159.08
> view matrix models
> #1,0.85104,-0.5248,0.017847,109.53,-0.41693,-0.69599,-0.58461,446.69,0.31922,0.49008,-0.81112,156.77
Drag select of 49 residues
> select add #1
13272 atoms, 13621 bonds, 3 pseudobonds, 1650 residues, 2 models selected
> view matrix models
> #1,0.85104,-0.5248,0.017847,199.95,-0.41693,-0.69599,-0.58461,507.11,0.31922,0.49008,-0.81112,194.53
> view matrix models
> #1,0.85104,-0.5248,0.017847,191.36,-0.41693,-0.69599,-0.58461,532.56,0.31922,0.49008,-0.81112,196.96
> view matrix models
> #1,0.85186,-0.52343,0.019012,183.59,-0.41516,-0.6969,-0.58479,527.41,0.31934,0.49026,-0.81096,194.65
> view matrix models
> #1,0.85186,-0.52343,0.019012,181.13,-0.41516,-0.6969,-0.58479,526.85,0.31934,0.49026,-0.81096,192.89
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
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 combine_3comp_W19-coot-8_real_space_refined_093_001.pdb, chain B
(#1) with ALL-coot-5.pdb, chain A (#2), sequence alignment score = 5977.5
RMSD between 570 pruned atom pairs is 1.364 angstroms; (across all 1313 pairs:
2.888)
> select subtract #1
Nothing selected
> close #2
> close #1
> open
> /Users/boskostojanovski/Desktop/Phenix/RealSpaceRefine_70/_Users_boskostojanovski_Combine_3comp_W15-Phenix_061_coot-01-coot-5.pdb
Chain information for
_Users_boskostojanovski_Combine_3comp_W15-Phenix_061_coot-01-coot-5.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> lighting simple
> hide atoms
> show cartoons
> open
> /Users/boskostojanovski/Desktop/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_002.pdb
Chain information for combine_3comp_W19-coot-8_real_space_refined_093_002.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> hide atoms
> show cartoons
> select #1/H#2/H
4060 atoms, 4170 bonds, 2 pseudobonds, 502 residues, 4 models selected
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> select #1/L#2/L
1692 atoms, 1734 bonds, 2 pseudobonds, 214 residues, 4 models selected
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> show atoms
> style stick
Changed 26552 atom styles
> color byhetero
> color #1 #00fdffff
> color byhetero
> hide #!1 models
> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/starting map
> and pdbs/comp_1350+1351_DEEP_W19.mrc"
Opened comp_1350+1351_DEEP_W19.mrc as #3, grid size 400,400,400, pixel 0.842,
shown at level -0.000457, step 2, values float32
> volume #3 step 1
> volume #3 color #b2b2b299
> volume #3 level 0.1691
> volume #3 level 0.203
> hide #!3 models
> show #!3 models
> volume #3 level 0.1
> volume #3 level 0.2187
> volume #3 level 0.1
> hide #!2 atoms
> hide #!3 models
> show #!2 atoms
> select #2/C
1863 atoms, 1904 bonds, 1 pseudobond, 235 residues, 2 models selected
> color (#!2 & sel) cornflower blue
> select clear
> select #2/C
1863 atoms, 1904 bonds, 1 pseudobond, 235 residues, 2 models selected
> color (#!2 & sel) dim gray
> color (#!2 & sel) light sea green
> color (#!2 & sel) byhetero
> view matrix models
> #2,0.97758,0.17103,0.12282,-44.76,-0.1681,0.98519,-0.033903,35.494,-0.1268,0.012496,0.99185,20.002
> view matrix models
> #2,0.97586,0.17745,0.12731,-46.276,-0.1743,0.98405,-0.035587,36.971,-0.1316,0.012538,0.99122,20.882
> select clear
> select #1/A#2/A
1364 atoms, 1396 bonds, 182 residues, 2 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> view matrix models
> #1,0.80061,0.18606,-0.56957,93.121,-0.10933,0.97997,0.16644,-5.4978,0.58913,-0.070985,0.80492,-53.287,#2,0.82381,0.31802,-0.46926,51.057,-0.2994,0.94703,0.11619,39.267,0.48136,0.04478,0.87538,-66.366
> view matrix models
> #1,0.99832,-0.057243,0.0090093,8.3722,0.057848,0.97537,-0.21286,28.79,0.0033973,0.21302,0.97704,-32.275,#2,0.98301,0.12093,0.13807,-39.754,-0.08554,0.96741,-0.23833,57.729,-0.16239,0.22248,0.96132,-4.1548
> view matrix models
> #1,0.99822,-0.033727,0.049148,-1.9589,0.044083,0.97269,-0.22787,33.896,-0.040121,0.22963,0.97245,-27.177,#2,0.97354,0.14456,0.177,-48.373,-0.096531,0.96214,-0.25487,63.059,-0.20715,0.23104,0.95064,3.475
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99822,-0.033727,0.049148,-2.5065,0.044083,0.97269,-0.22787,34.907,-0.040121,0.22963,0.97245,-28.718,#2,0.97354,0.14456,0.177,-48.921,-0.096531,0.96214,-0.25487,64.07,-0.20715,0.23104,0.95064,1.9346
> view matrix models
> #1,0.99822,-0.033727,0.049148,-4.6563,0.044083,0.97269,-0.22787,36.683,-0.040121,0.22963,0.97245,-32.962,#2,0.97354,0.14456,0.177,-51.071,-0.096531,0.96214,-0.25487,65.846,-0.20715,0.23104,0.95064,-2.3092
> view matrix models
> #1,0.99822,-0.033727,0.049148,-7.0285,0.044083,0.97269,-0.22787,38.42,-0.040121,0.22963,0.97245,-35.776,#2,0.97354,0.14456,0.177,-53.443,-0.096531,0.96214,-0.25487,67.582,-0.20715,0.23104,0.95064,-5.1237
> view matrix models
> #1,0.99822,-0.033727,0.049148,-3.3795,0.044083,0.97269,-0.22787,37.208,-0.040121,0.22963,0.97245,-33.256,#2,0.97354,0.14456,0.177,-49.794,-0.096531,0.96214,-0.25487,66.371,-0.20715,0.23104,0.95064,-2.603
> view matrix models
> #1,0.99822,-0.033727,0.049148,-3.1897,0.044083,0.97269,-0.22787,37.509,-0.040121,0.22963,0.97245,-32.712,#2,0.97354,0.14456,0.177,-49.604,-0.096531,0.96214,-0.25487,66.672,-0.20715,0.23104,0.95064,-2.0598
> view matrix models
> #1,0.99822,-0.033727,0.049148,-5.4855,0.044083,0.97269,-0.22787,37.973,-0.040121,0.22963,0.97245,-21.903,#2,0.97354,0.14456,0.177,-51.9,-0.096531,0.96214,-0.25487,67.136,-0.20715,0.23104,0.95064,8.7496
> view matrix models
> #1,0.99822,-0.033727,0.049148,-7.1223,0.044083,0.97269,-0.22787,38.247,-0.040121,0.22963,0.97245,-13.924,#2,0.97354,0.14456,0.177,-53.537,-0.096531,0.96214,-0.25487,67.41,-0.20715,0.23104,0.95064,16.729
> view matrix models
> #1,0.99822,-0.033727,0.049148,-3.4819,0.044083,0.97269,-0.22787,42.357,-0.040121,0.22963,0.97245,-8.5176,#2,0.97354,0.14456,0.177,-49.896,-0.096531,0.96214,-0.25487,71.52,-0.20715,0.23104,0.95064,22.135
> view matrix models
> #1,0.99822,-0.033727,0.049148,0.74602,0.044083,0.97269,-0.22787,47.599,-0.040121,0.22963,0.97245,-4.9909,#2,0.97354,0.14456,0.177,-45.669,-0.096531,0.96214,-0.25487,76.762,-0.20715,0.23104,0.95064,25.662
> view matrix models
> #1,0.99822,-0.033727,0.049148,3.608,0.044083,0.97269,-0.22787,50.919,-0.040121,0.22963,0.97245,-4.1406,#2,0.97354,0.14456,0.177,-42.807,-0.096531,0.96214,-0.25487,80.082,-0.20715,0.23104,0.95064,26.512
> view matrix models
> #1,0.99822,-0.033727,0.049148,4.9944,0.044083,0.97269,-0.22787,52.422,-0.040121,0.22963,0.97245,-3.6535,#2,0.97354,0.14456,0.177,-41.42,-0.096531,0.96214,-0.25487,81.585,-0.20715,0.23104,0.95064,26.999
> view matrix models
> #1,0.99822,-0.033727,0.049148,5.3424,0.044083,0.97269,-0.22787,53.718,-0.040121,0.22963,0.97245,-3.5568,#2,0.97354,0.14456,0.177,-41.072,-0.096531,0.96214,-0.25487,82.881,-0.20715,0.23104,0.95064,27.096
> view matrix models
> #1,0.99822,-0.033727,0.049148,6.9491,0.044083,0.97269,-0.22787,53.339,-0.040121,0.22963,0.97245,-2.9063,#2,0.97354,0.14456,0.177,-39.465,-0.096531,0.96214,-0.25487,82.502,-0.20715,0.23104,0.95064,27.746
> view matrix models
> #1,0.99822,-0.033727,0.049148,6.1419,0.044083,0.97269,-0.22787,54.528,-0.040121,0.22963,0.97245,-4.0811,#2,0.97354,0.14456,0.177,-40.273,-0.096531,0.96214,-0.25487,83.691,-0.20715,0.23104,0.95064,26.571
> view matrix models
> #1,0.99822,-0.033727,0.049148,4.0916,0.044083,0.97269,-0.22787,56.557,-0.040121,0.22963,0.97245,-5.991,#2,0.97354,0.14456,0.177,-42.323,-0.096531,0.96214,-0.25487,85.719,-0.20715,0.23104,0.95064,24.661
> view matrix models
> #1,0.99822,-0.033727,0.049148,5.9956,0.044083,0.97269,-0.22787,54.443,-0.040121,0.22963,0.97245,-8.1451,#2,0.97354,0.14456,0.177,-40.419,-0.096531,0.96214,-0.25487,83.606,-0.20715,0.23104,0.95064,22.507
> view matrix models
> #1,0.99822,-0.033727,0.049148,6.9912,0.044083,0.97269,-0.22787,53.413,-0.040121,0.22963,0.97245,-9.7917,#2,0.97354,0.14456,0.177,-39.423,-0.096531,0.96214,-0.25487,82.576,-0.20715,0.23104,0.95064,20.861
> view matrix models
> #1,0.99822,-0.033727,0.049148,11.179,0.044083,0.97269,-0.22787,54.604,-0.040121,0.22963,0.97245,-14.27,#2,0.97354,0.14456,0.177,-35.235,-0.096531,0.96214,-0.25487,83.767,-0.20715,0.23104,0.95064,16.383
> view matrix models
> #1,0.99822,-0.033727,0.049148,12.637,0.044083,0.97269,-0.22787,52.593,-0.040121,0.22963,0.97245,-12.062,#2,0.97354,0.14456,0.177,-33.778,-0.096531,0.96214,-0.25487,81.756,-0.20715,0.23104,0.95064,18.59
> view matrix models
> #1,0.99822,-0.033727,0.049148,9.9151,0.044083,0.97269,-0.22787,49.097,-0.040121,0.22963,0.97245,-14.274,#2,0.97354,0.14456,0.177,-36.499,-0.096531,0.96214,-0.25487,78.26,-0.20715,0.23104,0.95064,16.379
> view matrix models
> #1,0.99822,-0.033727,0.049148,6.7218,0.044083,0.97269,-0.22787,45.214,-0.040121,0.22963,0.97245,-16.455,#2,0.97354,0.14456,0.177,-39.693,-0.096531,0.96214,-0.25487,74.377,-0.20715,0.23104,0.95064,14.198
> view matrix models
> #1,0.99822,-0.033727,0.049148,2.925,0.044083,0.97269,-0.22787,40.931,-0.040121,0.22963,0.97245,-18.418,#2,0.97354,0.14456,0.177,-43.49,-0.096531,0.96214,-0.25487,70.094,-0.20715,0.23104,0.95064,12.234
> view matrix models
> #1,0.99822,-0.033727,0.049148,1.8442,0.044083,0.97269,-0.22787,49.379,-0.040121,0.22963,0.97245,-19.511,#2,0.97354,0.14456,0.177,-44.57,-0.096531,0.96214,-0.25487,78.542,-0.20715,0.23104,0.95064,11.142
> view matrix models
> #1,0.99822,-0.033727,0.049148,3.0466,0.044083,0.97269,-0.22787,51.821,-0.040121,0.22963,0.97245,-17.527,#2,0.97354,0.14456,0.177,-43.368,-0.096531,0.96214,-0.25487,80.983,-0.20715,0.23104,0.95064,13.126
> view matrix models
> #1,0.99822,-0.033727,0.049148,2.9203,0.044083,0.97269,-0.22787,54.108,-0.040121,0.22963,0.97245,-16.716,#2,0.97354,0.14456,0.177,-43.494,-0.096531,0.96214,-0.25487,83.271,-0.20715,0.23104,0.95064,13.936
> view matrix models
> #1,0.99822,-0.033727,0.049148,3.4591,0.044083,0.97269,-0.22787,54.231,-0.040121,0.22963,0.97245,-17.89,#2,0.97354,0.14456,0.177,-42.955,-0.096531,0.96214,-0.25487,83.394,-0.20715,0.23104,0.95064,12.762
> view matrix models
> #1,0.99822,-0.033727,0.049148,3.6158,0.044083,0.97269,-0.22787,54.244,-0.040121,0.22963,0.97245,-18.432,#2,0.97354,0.14456,0.177,-42.799,-0.096531,0.96214,-0.25487,83.407,-0.20715,0.23104,0.95064,12.22
> view matrix models
> #1,0.99822,-0.033727,0.049148,4.5996,0.044083,0.97269,-0.22787,55.332,-0.040121,0.22963,0.97245,-18.34,#2,0.97354,0.14456,0.177,-41.815,-0.096531,0.96214,-0.25487,84.495,-0.20715,0.23104,0.95064,12.312
> view matrix models
> #1,0.99822,-0.033727,0.049148,3.6812,0.044083,0.97269,-0.22787,55.631,-0.040121,0.22963,0.97245,-15.685,#2,0.97354,0.14456,0.177,-42.733,-0.096531,0.96214,-0.25487,84.794,-0.20715,0.23104,0.95064,14.967
> view matrix models
> #1,0.99822,-0.033727,0.049148,4.872,0.044083,0.97269,-0.22787,56.429,-0.040121,0.22963,0.97245,-17.644,#2,0.97354,0.14456,0.177,-41.543,-0.096531,0.96214,-0.25487,85.592,-0.20715,0.23104,0.95064,13.009
> view matrix models
> #1,0.99822,-0.033727,0.049148,4.8129,0.044083,0.97269,-0.22787,55.758,-0.040121,0.22963,0.97245,-19.492,#2,0.97354,0.14456,0.177,-41.602,-0.096531,0.96214,-0.25487,84.921,-0.20715,0.23104,0.95064,11.161
> hide #!2 models
> select add #2
13954 atoms, 14319 bonds, 3 pseudobonds, 1741 residues, 3 models selected
> select add #1
26552 atoms, 27251 bonds, 5 pseudobonds, 3301 residues, 4 models selected
> select subtract #1
13272 atoms, 13621 bonds, 3 pseudobonds, 1650 residues, 2 models selected
> select subtract #2
Nothing selected
> open 7tpp
7tpp title:
Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom
resolution [more info...]
Chain information for 7tpp #4
---
Chain | Description | UniProt
A | Factor X light chain | FA10_HUMAN 1-139
B | Activated factor Xa heavy chain | FA10_HUMAN 195-448
C | Coagulation factor Va | FA5_HUMAN 1-709
D | Coagulation factor Va | FA5_HUMAN 1546-2196
E | Prothrombin | THRB_HUMAN 1-579
> show #!4 cartoons
> hide #!4 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:356
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/B:356
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> ui tool show "Show Sequence Viewer"
> sequence chain #4/E
Alignment identifier is 4/E
> select #4/E:316
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/E:316-317
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> view matrix models #4,1,0,0,-4.2459,0,1,0,3.48,0,0,1,7.2033
> view matrix models #4,1,0,0,-4.5692,0,1,0,5.8107,0,0,1,10.848
> view matrix models #4,1,0,0,-2.4935,0,1,0,-2.0883,0,0,1,14.015
> view matrix models #4,1,0,0,0.8336,0,1,0,-20.727,0,0,1,12.47
> view matrix models #4,1,0,0,1.3737,0,1,0,-26.846,0,0,1,12.043
> select #4/E:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/E:318-320
23 atoms, 22 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 23 atom styles
> select #4/B:373
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:373
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> close #4
> show #!2 models
> view orient
> hide #!2 atoms
> show #!2 atoms
> hide #!2 atoms
> show #!3 models
> show #!1 models
> hide #!1 models
> close #3
> show #!1 models
> close #2
> close #1
> open
> /Users/boskostojanovski/Desktop/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_004.pdb
Chain information for combine_3comp_W19-coot-8_real_space_refined_093_004.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
> lighting simple
> show cartoons
> hide atoms
> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/starting map
> and pdbs/comp_1350+1351_DEEP_W19.mrc"
Opened comp_1350+1351_DEEP_W19.mrc as #2, grid size 400,400,400, pixel 0.842,
shown at level -0.000457, step 2, values float32
> volume #2 step 1
> volume #2 color #b2b2b299
> volume #2 level 0.1
> show atoms
> style stick
Changed 16148 atom styles
> color #1 #00fdffff
> color #1 #fffc79ff
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
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
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 575 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: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
System Firmware Version: 529.120.1.0.0
OS Loader Version: 577.140.2~22
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 14 days, 6 hours, 1 minute
Graphics/Displays:
Radeon Pro 575:
Chipset Model: Radeon Pro 575
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c4
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1P-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG UltraFine:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 201NTRLKF070
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
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 , 14 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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