![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16347 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
I have a bunch of programs open, I was working on a different one when ChimeraX crashed.
Fatal Python error: Segmentation fault
Current thread 0x00000001f8474f40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 57)
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{
"uptime" : 820000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,10",
"coalitionID" : 75879,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-11-20 12:57:42.0176 -0800",
"codeSigningMonitor" : 1,
"incident" : "48D858B6-3694-4F29-A68B-FA057519E96C",
"pid" : 98195,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-18 14:25:58.9385 -0800",
"procStartAbsTime" : 18559191883898,
"procExitAbsTime" : 19767044176037,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E86FC26C-28CC-5EEB-A07C-067736B39E4C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "757FF526-C3CD-C48D-1A97-DEC7F6A548D6",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 11697,
"sleepWakeUUID" : "826F9A8A-CBA9-4BA1-BA63-7DD9BAD0C892",
"sip" : "enabled",
"vmRegionInfo" : "0x3b95400ca528 is not in any region. Bytes after previous region: 65031174399273 Bytes before following region: 40040905530072\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000bb95400ca528","rawCodes":[1,206249699091752],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000bb95400ca528 -> 0x00003b95400ca528 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":98195},
"vmregioninfo" : "0x3b95400ca528 is not in any region. Bytes after previous region: 65031174399273 Bytes before following region: 40040905530072\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=7.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=7.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 1744K 78 \nColorSync 656K 31 \nCoreAnimation 4416K 252 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 5888K 62 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 6.8G 200 \nMALLOC guard page 192K 12 \nMALLOC_LARGE (reserved) 122.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 816K 51 \nStack 162.3M 52 \nStack Guard 56.0M 1 \nVM_ALLOCATE 358.8M 415 \nVM_ALLOCATE (reserved) 320.0M 4 reserved VM address space (unallocated)\n__AUTH 2210K 407 \n__AUTH_CONST 31.9M 626 \n__CTF 824 1 \n__DATA 21.9M 771 \n__DATA_CONST 42.5M 782 \n__DATA_DIRTY 2032K 234 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 554.0M 151 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 939.3M 799 \ndyld private memory 272K 2 \nmapped file 595.6M 121 \nshared memory 3280K 33 \n=========== ======= ======= \nTOTAL 10.0G 5113 \nTOTAL, minus reserved VM space 9.6G 5113 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "dc33f7fa6a1e3bcffcdfeaa4db4e8813ced7b940",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "642da32dea3b2418c750f848",
"factorPackIds" : {
},
"deploymentId" : 240000004
},
{
"rolloutId" : "648a2601f74c42732876cb5b",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "6733fcb357a33f0bf26912cf"
},
"deploymentId" : 240000272
}
],
"experiments" : [
{
"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: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/will/Documents/Marletta_Lab/Houghton/Kim_Paper/Kim_Work/Open/Cyc_Open_Files/Ms_sGC_BC122S_Ext_85pix.mrc
Opened Ms_sGC_BC122S_Ext_85pix.mrc as #1, grid size 320,320,320, pixel 0.85,
shown at level 0.091, step 2, values float32
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color white
> set bgColor white
> volume #1 color #00efff98
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #1 level 0.1879
> volume #1 level 0.4786
> open
> /Users/will/Documents/Marletta_Lab/Houghton/Kim_Paper/Kim_Work/Closed/Unliganded_Closed_Files/J85_J92_combined.mrc
Opened J85_J92_combined.mrc as #2, grid size 320,320,320, pixel 0.942, shown
at level 0.00381, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> volume #2 level 0.9596
> volume #2 color #ff14f199
> open
> /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_cyc_20240415/RealSpaceRefine_8/KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px-
> Backbone_Trace_Done-coot-3_real_space_refined_008.pdb
Chain information for KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px-
Backbone_Trace_Done-coot-3_real_space_refined_008.pdb #3
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_20231023/RealSpaceRefine_53/HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb
Chain information for HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb
#4
---
Chain | Description
A | No description available
B | No description available
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Grpmeeting_maps.cxs
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> volume #1 level 0.5087
> volume #1 level 0.4786
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/active_J287.png
> width 1111 height 786 supersample 3
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!2 models
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive.png
> width 1111 height 786 supersample 3
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!2 models
> show #!3 models
> volume #1 level 0.4886
> close #4
> open
> /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_cyc_20240415/RealSpaceRefine_8/KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px-
> Backbone_Trace_Done-coot-4.pdb
Chain information for KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px-
Backbone_Trace_Done-coot-4.pdb #4
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_20231023/RealSpaceRefine_53/HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb
Chain information for HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb
#5
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_cyc_20240415/RealSpaceRefine_8/KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px-
> Backbone_Trace_Done-coot-4.pdb
Chain information for KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px-
Backbone_Trace_Done-coot-4.pdb #6
---
Chain | Description
A | No description available
B | No description available
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> close #6
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> close #3
> hide #!1 models
> select #4/C
32 atoms, 34 bonds, 1 residue, 1 model selected
> color sel forest green
> color sel byhetero
> ui mousemode right select
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 60 bonds, 1 residue, 1 model selected
> color sel purple
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel dark gray
> color sel byhetero
> select clear
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Grpmeeting_maps.cxs
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select clear
> select #4/C and #4/B:601-602
Expected a keyword
> select #4/C or #4/B:601-602
Expected a keyword
> select #4/C or /B:601-602
Expected a keyword
> select #4/C or select #4/B:601-602
Expected a keyword
> select #4/C,#4/B:601-602
Expected an objects specifier or a keyword
> select #4/C/B:601-602
131 atoms, 140 bonds, 4 pseudobonds, 3 residues, 2 models selected
> name frozen ligands sel
> show #!1 models
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #1 near #4 distance 5.1
> color single #1
> color zone #1 near sel distance 5.1
> color zone #1 near sel distance 1.25
> color zone #1 near sel distance 1.23
> color zone #1 near sel distance 1.21
> color zone #1 near sel distance 1.23
> volume #1 level 0.5925
> color zone #1 near sel distance 1.24
> color zone #1 near sel distance 2.84
> volume splitbyzone #1
Opened Ms_sGC_BC122S_Ext_85pix.mrc 0 as #3.1, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 1 as #3.2, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 2 as #3.3, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 3 as #3.4, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 4 as #3.5, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 5 as #3.6, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 6 as #3.7, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 7 as #3.8, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 8 as #3.9, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 9 as #3.10, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
> close #3.10
> close #3.8
> close #3.7
> close #3.6
> close #3.5
> close #3.4
> close #3.3
> close #3.9
> close #3
> show #!1 models
> color single #1
> hide #!1 models
> select clear
> select #4/B:601@CBD
1 atom, 1 residue, 1 model selected
> select #4/B:601@CBD
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
4459 atoms, 4553 bonds, 560 residues, 1 model selected
> color sel gray
> undo
> select down
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel gray
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 60 bonds, 1 residue, 1 model selected
> color sel purple
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
32 atoms, 34 bonds, 1 residue, 1 model selected
> color sel forest green
> select #4/C/B:601-602
131 atoms, 140 bonds, 4 pseudobonds, 3 residues, 2 models selected
> show #!1 models
> color zone #1 near sel distance 2.84
> color zone #1 near sel distance 2.94
> color zone #1 near sel distance 2.84
> color zone #1 near sel distance 2.8
> color zone #1 near sel distance 2.85
> color zone #1 near sel distance 2.8
> color zone #1 near sel distance 2.86
> volume splitbyzone #1
Opened Ms_sGC_BC122S_Ext_85pix.mrc 0 as #3.1, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 1 as #3.2, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 2 as #3.3, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
Opened Ms_sGC_BC122S_Ext_85pix.mrc 3 as #3.4, grid size 320,320,320, pixel
0.85, shown at level 0.592, step 1, values float32
> select clear
> transparency #4#3.2-4#!3 60
> color #4#3.2-4#!3 byhetero
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Grpmeeting_maps.cxs
> includeMaps true
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/active_G2P.png
> width 1136 height 786 supersample 3
> hide #!3.3 models
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_heme.png
> width 1136 height 786 supersample 3
> show #!3.3 models
> hide #!3.2 models
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_cyc.png
> width 1136 height 786 supersample 3
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_cyc2.png
> width 1136 height 786 supersample 3
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_cyc3.png
> width 1136 height 786 supersample 3
> show #!1 models
> hide #!3.3 models
> hide #!3 models
> hide #!3.4 models
> hide #!4 models
> show #!4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> color single #1
> volume #1 level 0.441
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_with_model.png
> width 1136 height 786 supersample 3
> show #!3.4 models
> volume #1 level 0.5384
> volume #3.4 level 0.4535
> volume #3.1 level 0.7548
> volume #3.1 level 0.4626
> volume #3.1 level 0.5275
> volume #1 level 0.6249
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/active_G2P_over.png
> width 1136 height 786 supersample 3
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_nolig/C122S_nolig_refine_aligned.mrc
Opened C122S_nolig_refine_aligned.mrc as #6, grid size 64,64,64, pixel 6.33,
shown at level 0.000834, step 1, values float32
> open
> /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_nolig/8hbe_centered.pdb
Chain information for 8hbe_centered.pdb #7
---
Chain | Description
A | No description available
B | No description available
> volume #6 color #b2ffb2aa
> volume #6 color #b2ffb2ab
> volume #6 level 0.006581
> open
> /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_cyc/C122S_cyc_refine_aligned.mrc
Opened C122S_cyc_refine_aligned.mrc as #8, grid size 64,64,64, pixel 6.33,
shown at level 0.000719, step 1, values float32
> volume #8 level 0.005941
> volume #8 color #e5bf99a8
> volume #6 level 0.0153
> volume #8 level 0.007477
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.39844,0.90908,0.12177,14.843,0.89861,0.36032,0.25034,-7.65,0.1837,0.20916,-0.96047,-13.123
> view matrix models
> #8,0.55373,0.76355,0.33222,4.7091,0.67378,-0.64529,0.36003,-1.0228,0.48928,0.024486,-0.87178,-15.813
> view matrix models
> #8,-0.35769,0.9313,-0.068832,13.28,0.88889,0.36214,0.28058,-7.3795,0.28623,0.039175,-0.95736,-13.81
> view matrix models
> #8,0.14553,0.98158,0.12378,7.93,0.93262,-0.17786,0.31399,-5.9744,0.33023,0.069741,-0.94132,-14.368
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.14553,0.98158,0.12378,2.1043,0.93262,-0.17786,0.31399,-11.166,0.33023,0.069741,-0.94132,-0.96409
> view matrix models
> #8,0.14553,0.98158,0.12378,-0.35155,0.93262,-0.17786,0.31399,-15.366,0.33023,0.069741,-0.94132,0.5689
> view matrix models
> #8,0.14553,0.98158,0.12378,0.2831,0.93262,-0.17786,0.31399,-6.1745,0.33023,0.069741,-0.94132,-2.0622
> view matrix models
> #8,0.14553,0.98158,0.12378,0.39841,0.93262,-0.17786,0.31399,-3.703,0.33023,0.069741,-0.94132,-8.6659
> select subtract #8
Nothing selected
> show #!3.1 models
> hide #!3.1 models
> hide #!1 models
> show #!2 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!4 models
> hide #!4 models
> show #!5 models
> color #5 #15fd1fff
> color #5 #3ae9fdff
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_with_model.png
> width 1136 height 786 supersample 3
> ui mousemode right clip
> ui mousemode right zone
> ui tool show "Side View"
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_empty_basket.png
> width 1136 height 786 supersample 3
> select #5/C/B:601
75 atoms, 78 bonds, 4 pseudobonds, 1 residue, 2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Surface Color"
> color (#!5 & sel) gray
> ui tool show "Surface Color"
> ui tool show "Surface Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface zone #2 nearAtoms #5 distance 5.65
> surface zone #2 nearAtoms sel distance 5.65
> surface zone #2 nearAtoms sel distance 4.45
> surface zone #2 nearAtoms sel distance 1.95
> color (#!5 & sel) gray
> surface unzone #2
> surface zone #2 nearAtoms sel distance 1.95
> surface unzone #2
> ui tool show "Surface Zone"
> ui tool show "Surface Color"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Color Zone"
> color zone #2 near #5 distance 1.8
> color single #2
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #2 near sel distance 1.8
> volume splitbyzone #2
Opened J85_J92_combined.mrc 0 as #9.1, grid size 320,320,320, pixel 0.942,
shown at level 0.96, step 1, values float32
Opened J85_J92_combined.mrc 1 as #9.2, grid size 320,320,320, pixel 0.942,
shown at level 0.96, step 1, values float32
> hide #!9.2 models
> show #!9.2 models
> hide #!9.1 models
> show #!9.1 models
> color (#!5 & sel) forest green
> color (#!5 & sel) byhetero
> color #9 #b2b2b293 models
> color #9 #b2b2b294 models
> hide #!9.1 models
> show #!9.1 models
> color #9 #b2b2b2ff models
> color #9.1 #ff00f9ff models
> color #9.1 #ff00f998 models
> color #9.1 #ff00f980 models
> color #9.2 #80808098 models
> color #9.2 #80808099 models
> hide #!9.1 models
> select clear
> color #5#9.2#!3,9 byhetero
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_heme.png
> width 905 height 786 supersample 3
> show #!7 models
> show #!6 models
> show #!8 models
> open
> /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_G2P_cyc_BIFT/C122S_G2P_cyc2_refine_aligned.mrc
Opened C122S_G2P_cyc2_refine_aligned.mrc as #10, grid size 64,64,64, pixel
8.73, shown at level 2.46e-05, step 1, values float32
> volume #10 level 0.004475
> volume #10 color #b2b2b2b0
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> hide #!8 models
> select add #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.83853,-0.54423,0.026125,2.3156,-0.54441,0.83882,0.00026625,0.69237,-0.022059,-0.013999,-0.99966,1.8163
> view matrix models
> #10,-0.94876,0.049305,0.31212,-0.88255,0.032066,0.99768,-0.06013,0.070151,-0.31436,-0.047041,-0.94814,1.8792
> view matrix models
> #10,-0.99341,0.11247,-0.022269,-0.90955,0.11405,0.98927,-0.091359,0.15437,0.011755,-0.093297,-0.99557,2.2101
> view matrix models
> #10,-0.98932,0.13523,-0.054441,-0.99286,0.13998,0.98551,-0.095802,0.18167,0.040697,-0.1024,-0.99391,2.259
> open /Users/will/Documents/Marletta_Lab/sGC/Msexta_sGC/PDB_Files/8hbf.pdb
8hbf.pdb title:
Structure of human soluble guanylate cyclase In the No+rio state At 3.1
angstrom [more info...]
Chain information for 8hbf.pdb #11
---
Chain | Description | UniProt
A | guanylate cyclase soluble subunit α-1 | GCYA1_HUMAN 1-690
B | guanylate cyclase soluble subunit β-1 | GCYB1_HUMAN 1-619
Non-standard residues in 8hbf.pdb #11
---
G2P — phosphomethylphosphonic acid guanylate ester
GZO — methyl
~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-B]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-
carbamate
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NO — nitric oxide (nitrogen monoxide)
2 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #11
8446 atoms, 8614 bonds, 25 pseudobonds, 1101 residues, 5 models selected
> select subtract #10
8446 atoms, 8614 bonds, 25 pseudobonds, 1101 residues, 3 models selected
> view matrix models
> #11,-0.63869,0.66485,-0.38737,189.88,0.70973,0.70349,0.037211,-62.878,0.29725,-0.25116,-0.92117,260.87
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.63869,0.66485,-0.38737,187.72,0.70973,0.70349,0.037211,-192.52,0.29725,-0.25116,-0.92117,99.205
> view matrix models
> #11,-0.63869,0.66485,-0.38737,57.146,0.70973,0.70349,0.037211,-179.24,0.29725,-0.25116,-0.92117,123.08
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.80429,-0.59423,0.00041531,184.55,-0.52833,0.71541,0.45722,-73.435,-0.272,0.36752,-0.88935,116.65
> view matrix models
> #11,0.85758,0.06966,-0.50962,-51.109,0.25894,-0.91455,0.31073,47.886,-0.44442,-0.39844,-0.80233,224.61
> view matrix models
> #11,0.96296,0.22257,-0.15219,-134.65,0.26528,-0.88302,0.38717,32.341,-0.048215,-0.41321,-0.90936,188.3
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.96296,0.22257,-0.15219,-133.9,0.26528,-0.88302,0.38717,26.842,-0.048215,-0.41321,-0.90936,183.82
> volume #10 level 0.007047
> view matrix models
> #11,0.96296,0.22257,-0.15219,-129.78,0.26528,-0.88302,0.38717,13.912,-0.048215,-0.41321,-0.90936,169.98
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.94568,-0.30285,-0.11821,-65.669,-0.21364,-0.85297,0.47623,61.895,-0.24506,-0.4251,-0.87134,192.58
> view matrix models
> #11,0.97242,0.23321,-0.0034054,-153.22,0.18478,-0.76141,0.62138,-23.477,0.14232,-0.60487,-0.7835,151.08
> select subtract #11
Nothing selected
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!8 models
> hide #!10 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!7 models
> show #!7 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!6 models
> hide #!8 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.01061
Opened 8hbe_centered.pdb map 5 as #12, grid size 56,68,101, pixel 1.67, shown
at level 0.1, step 1, values float32
> fitmap #7 inMap #6 resolution 5
Fit map 8hbe_centered.pdb map 5 in map C122S_nolig_refine_aligned.mrc using
32943 points
correlation = 0.7722, correlation about mean = 0.02628, overlap = 284.2
steps = 68, shift = 3.96, angle = 5.47 degrees
Position of 8hbe_centered.pdb map 5 (#12) relative to
C122S_nolig_refine_aligned.mrc (#6) coordinates:
Matrix rotation and translation
0.99821929 -0.05963242 -0.00148866 1.98975524
0.05957753 0.99544092 0.07448421 -0.23286547
-0.00295980 -0.07444027 0.99722108 3.41000515
Axis -0.78066563 0.00771176 0.62490136
Axis point 0.00000000 40.76298503 5.68103763
Rotation angle (degrees) 5.47336510
Shift along axis 0.57578752
Average map value = 0.02434 for 8610 atoms, 1297 outside contour
> hide #!7 models
> show #!7 models
> show #!8 models
> fitmap #8 inMap #12
Fit map C122S_cyc_refine_aligned.mrc in map 8hbe_centered.pdb map 5 using 1800
points
correlation = 0.5271, correlation about mean = 0.1255, overlap = 4.607
steps = 164, shift = 5.96, angle = 14.9 degrees
Position of C122S_cyc_refine_aligned.mrc (#8) relative to 8hbe_centered.pdb
map 5 (#12) coordinates:
Matrix rotation and translation
0.00119032 0.99985513 -0.01697929 0.58507699
0.90747006 0.00605324 0.42007314 -2.49405624
0.42011507 -0.01590822 -0.90733139 -6.83424330
Axis -0.69842784 -0.70021082 -0.14799786
Axis point 2.27774967 0.00000000 -2.89915643
Rotation angle (degrees) 161.81318786
Shift along axis 2.34918445
> hide #!6 models
> show #!11 models
> hide #!11 models
> show #!11 models
> ui mousemode right "move picked models"
> select add #11
8446 atoms, 8614 bonds, 25 pseudobonds, 1101 residues, 3 models selected
> view matrix models
> #11,0.97242,0.23321,-0.0034054,-149.98,0.18478,-0.76141,0.62138,-26.343,0.14232,-0.60487,-0.7835,165.66
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.42126,-0.85269,0.30896,17.774,-0.90474,-0.41881,0.077733,152.55,0.063113,-0.31227,-0.94789,162.24
> view matrix models
> #11,0.95358,0.26424,0.14446,-172.08,0.13751,-0.80882,0.57176,-7.0489,0.26793,-0.52535,-0.8076,142.11
> view matrix models
> #11,0.10425,-0.98861,-0.10856,135.97,-0.99454,-0.10414,-0.0067043,136.56,-0.0046779,0.10866,-0.99407,124.48
> view matrix models
> #11,0.98331,-0.17011,-0.064475,-91.811,-0.16072,-0.97838,0.13016,116.26,-0.085222,-0.11762,-0.98939,163.3
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.98331,-0.17011,-0.064475,-91.758,-0.16072,-0.97838,0.13016,132.58,-0.085222,-0.11762,-0.98939,176.91
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.98334,-0.16998,-0.064396,-91.788,-0.16066,-0.97847,0.12955,132.67,-0.08503,-0.11704,-0.98948,176.82
Opened 8hbf.pdb map 5 as #13, grid size 50,76,101, pixel 1.67, shown at level
0.101, step 1, values float32
Opened 8hbf.pdb map 5 as #14, grid size 50,76,101, pixel 1.67, shown at level
0.101, step 1, values float32
> fitmap #11 inMap #12 resolution 5
Fit map 8hbf.pdb map 5 in map 8hbe_centered.pdb map 5 using 32157 points
correlation = 0.6743, correlation about mean = 0.1197, overlap = 2513
steps = 2000, shift = 13.3, angle = 36.1 degrees
Position of 8hbf.pdb map 5 (#14) relative to 8hbe_centered.pdb map 5 (#12)
coordinates:
Matrix rotation and translation
0.75669742 -0.62005543 -0.20722035 16.04564334
-0.65034173 -0.74631724 -0.14165523 215.62017722
-0.06681803 0.24195419 -0.96798426 116.30544316
Axis 0.93650708 -0.34276471 -0.07393805
Axis point 0.00000000 104.59522449 69.42301043
Rotation angle (degrees) 168.18170472
Shift along axis -67.47952656
Average map value = 0.2319 for 8381 atoms, 3371 outside contour
> show #!10 models
> select subtract #11
Nothing selected
> fitmap #10 inMap #14
Fit map C122S_G2P_cyc2_refine_aligned.mrc in map 8hbf.pdb map 5 using 650
points
correlation = 0.6168, correlation about mean = 0.3939, overlap = 2.12
steps = 136, shift = 2.16, angle = 4.56 degrees
Position of C122S_G2P_cyc2_refine_aligned.mrc (#10) relative to 8hbf.pdb map 5
(#14) coordinates:
Matrix rotation and translation
-0.90689824 -0.42099990 0.01716624 134.62497110
0.40917528 -0.88968597 -0.20256965 142.85406676
0.10055437 -0.17668606 0.97911739 147.19850089
Axis 0.03100745 -0.09989544 0.99451468
Axis point 47.81607757 93.15540942 0.00000000
Rotation angle (degrees) 155.33090072
Shift along axis 136.29497662
> fitmap #10 inMap #14
Fit map C122S_G2P_cyc2_refine_aligned.mrc in map 8hbf.pdb map 5 using 650
points
correlation = 0.6171, correlation about mean = 0.3947, overlap = 2.12
steps = 48, shift = 0.0346, angle = 0.11 degrees
Position of C122S_G2P_cyc2_refine_aligned.mrc (#10) relative to 8hbf.pdb map 5
(#14) coordinates:
Matrix rotation and translation
-0.90767371 -0.41934549 0.01666709 134.59443001
0.40760914 -0.89033394 -0.20287992 142.84223340
0.09991605 -0.17735511 0.97906177 147.18821727
Axis 0.03069633 -0.10011586 0.99450216
Axis point 47.89583841 93.10618147 0.00000000
Rotation angle (degrees) 155.43261737
Shift along axis 136.20978240
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> select add #10
2 models selected
> view matrix models
> #10,-0.97412,0.14087,-0.17677,1.3205,0.15374,0.98621,-0.06133,0.17319,0.1657,-0.086921,-0.98234,2.7739
> view matrix models
> #10,-0.6427,0.76177,-0.081537,-2.0193,0.76476,0.63158,-0.12752,2.3102,-0.045641,-0.14431,-0.98848,3.0308
> view matrix models
> #10,-0.95319,-0.075577,-0.29277,2.6348,-0.023658,0.98393,-0.17697,0.29687,0.30144,-0.16176,-0.93966,3.1489
> view matrix models
> #10,-0.96246,0.19276,-0.19111,1.0677,0.22951,0.95382,-0.1938,0.54738,0.14493,-0.23038,-0.96225,3.5026
> view matrix models
> #10,-0.93158,-0.24336,-0.27006,3.5004,-0.2036,0.96471,-0.16699,0.33729,0.30117,-0.10058,-0.94825,2.8357
> view matrix models
> #10,-0.53102,0.83766,-0.12781,-2.329,0.8354,0.49229,-0.24445,3.2294,-0.14184,-0.23658,-0.9612,3.4577
> view matrix models
> #10,-0.91978,0.071964,-0.38578,1.988,0.22423,0.90314,-0.36614,1.0519,0.32206,-0.42327,-0.84683,4.4155
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.91978,0.071964,-0.38578,5.8895,0.22423,0.90314,-0.36614,9.7635,0.32206,-0.42327,-0.84683,16.104
> fitmap #10 inMap #14
Fit map C122S_G2P_cyc2_refine_aligned.mrc in map 8hbf.pdb map 5 using 650
points
correlation = 0.6479, correlation about mean = 0.3999, overlap = 2.351
steps = 96, shift = 2.99, angle = 10.9 degrees
Position of C122S_G2P_cyc2_refine_aligned.mrc (#10) relative to 8hbf.pdb map 5
(#14) coordinates:
Matrix rotation and translation
-0.94725477 -0.32039190 -0.00757898 132.76811198
0.31141233 -0.92577745 0.21437930 135.61392817
-0.07570184 0.20071163 0.97672108 128.72113254
Axis -0.02150313 0.10717660 0.99400744
Axis point 57.87617404 72.00846116 0.00000000
Rotation angle (degrees) 161.46967157
Shift along axis 139.62947275
> select subtract #10
Nothing selected
> show #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2
2 models selected
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view orient
> view sel
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select #4/B:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #!9.2 models
> show #!9.2 models
> hide #!9 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9.2 models
> color #2 #ff50ec99 models
> color #2 #ff40e899 models
> color #2 #ff44dd99 models
> color #2 #ff00faff models
> color #2 #ff00fa9b models
> color #2 #ff00fa99 models
> color #2 #ff00fa80 models
> color #2 #ff00fa9a models
> color #2 #ff00fa99 models
> select #4/B:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> view matrix models #4,1,0,0,-0.13721,0,1,0,-0.076784,0,0,1,-2.4285
> view matrix models #4,1,0,0,0.013151,0,1,0,3.4421,0,0,1,2.4784
> select add #4
7309 atoms, 7470 bonds, 11 pseudobonds, 922 residues, 3 models selected
> select subtract #4
Nothing selected
> select #5/B:122
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> show (sel-residues & sidechain) target ab
> volume #2 level 0.6175
> ui tool show "Side View"
> select H
9056 atoms, 1159 residues, 2 models selected
> hide (#!5 & sel) target a
> select clear
> volume #2 color #ff00fa80
> volume #2 color #ff00fa73
> hide #!9 models
> hide #!5 models
> show #!5 models
> save
> /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_c122s.png
> width 753 height 805 supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,10
Model Number: MRX53LL/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 36 days, 2 hours, 14 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Acer S232HL:
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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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