![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16077 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.
Fatal Python error: Segmentation fault
Current thread 0x00000001ebb98f40 (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.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 62)
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{
"uptime" : 270000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 32209,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-10-06 00:27:31.0548 +0100",
"codeSigningMonitor" : 1,
"incident" : "1B6C1DD4-1951-4068-89D9-EF769B17D5C4",
"pid" : 52873,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-05 19:35:28.8394 +0100",
"procStartAbsTime" : 6335876266617,
"procExitAbsTime" : 6643992767187,
"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":"95EA9875-E798-50C2-A70E-4ADB9E064864","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "436138E8-7B98-5034-1A43-08D6C4D3F078",
"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" : 3842,
"sleepWakeUUID" : "11B08CCA-B400-45A8-9AEF-9AB13D637A6B",
"sip" : "enabled",
"vmRegionInfo" : "0x45a347a48a58 is not in any region. Bytes after previous region: 76086547614297 Bytes before following region: 28985532315048\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, 0x0000c5a347a48a58","rawCodes":[1,217305072306776],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000c5a347a48a58 -> 0x000045a347a48a58 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":52873},
"vmregioninfo" : "0x45a347a48a58 is not in any region. Bytes after previous region: 76086547614297 Bytes before following region: 28985532315048\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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"name" : "_lzma.cpython-311-darwin.so"
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"size" : 16384,
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
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"uuid" : "65172ede-2b95-337d-970f-ed6c4a217cb1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
{
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"size" : 16384,
"uuid" : "39aa96c6-b691-3e20-9540-292b9dd1c861",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
"source" : "P",
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"base" : 4312252416,
"size" : 81920,
"uuid" : "3b2e1e73-f5e1-3fa3-80b3-e46009060893",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
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"size" : 49152,
"uuid" : "51d31d0d-1dcc-31ad-b6c1-73d57e544a3a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4328849408,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 3948544,
"uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
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"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"uuid" : "71ff45b8-f14e-3666-9e96-6cf58315b91d",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6506688512,
"size" : 53248,
"uuid" : "e03e8478-6f5c-3d21-a79a-58408f514000",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6505234432,
"size" : 520184,
"uuid" : "d30f1830-93d0-3d0b-8cba-9544e84bfd5b",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6506897408,
"size" : 32744,
"uuid" : "b4bf9f89-31d7-3742-8ce7-ab3554f9f525",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
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"arch" : "arm64e",
"base" : 6566498304,
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20180992,
"uuid" : "7acbeef9-a453-3e4d-98ac-f9441d86e183",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.70.105"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6598713344,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4857856,
"uuid" : "2b8cc0cb-bced-39d7-aaca-5035567e114d",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6504927232,
"size" : 294912,
"uuid" : "1a1ce00a-89cd-36ba-9678-5038aedd0d8d",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
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"CFBundleShortVersionString" : "6.9",
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"size" : 5083136,
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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"size" : 2899968,
"uuid" : "4166f6cb-b599-306c-8568-823bd29a74c3",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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{
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"uuid" : "f635824e-318b-3f0c-842c-c369737f2b68",
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"uuid" : "aaa5636d-6f3f-3fa7-9f4a-cf966f0308fe",
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}
],
"sharedCache" : {
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 848K 34 \nColorSync 656K 31 \nCoreAnimation 2896K 142 \nCoreGraphics 48K 3 \nCoreUI image data 5440K 43 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.8G 96 \nMALLOC guard page 192K 12 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 153.8M 36 \nVM_ALLOCATE 214.7M 170 \nVM_ALLOCATE (reserved) 128.0M 4 reserved VM address space (unallocated)\n__AUTH 3602K 489 \n__AUTH_CONST 37.7M 723 \n__CTF 824 1 \n__DATA 27.7M 876 \n__DATA_CONST 47.9M 885 \n__DATA_DIRTY 2212K 264 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 555.4M 158 \n__OBJC_RO 71.9M 2 \n__OBJC_RW 2200K 1 \n__TEXT 1.1G 903 \ndyld private memory 592K 6 \nmapped file 275.1M 86 \nshared memory 3136K 24 \n=========== ======= ======= \nTOTAL 5.4G 5041 \nTOTAL, minus reserved VM space 5.3G 5041 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "6adeb57a55f13df3622dee06b3c3cc10cf749019",
"trialInfo" : {
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"experiments" : [
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}
}
===== 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/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/3ltm_A_A_solenoid.pdb"
Chain information for 3ltm_A_A_solenoid.pdb #1
---
Chain | Description
A | No description available
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/4gpm_A_A_solenoid.pdb"
Chain information for 4gpm_A_A_solenoid.pdb #2
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/4pjs_A_A_solenoid.pdb"
Chain information for 4pjs_A_A_solenoid.pdb #3
---
Chain | Description
A | No description available
90 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/4r5c_A_A_solenoid.pdb"
Chain information for 4r5c_A_A_solenoid.pdb #4
---
Chain | Description
A | No description available
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/5di5_A_A_solenoid.pdb"
Chain information for 5di5_A_A_solenoid.pdb #5
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/5i9d_A_A_solenoid.pdb"
Chain information for 5i9d_A_A_solenoid.pdb #6
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/6veh_A_A_solenoid.pdb"
Chain information for 6veh_A_A_solenoid.pdb #7
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/6xt4_A_A_solenoid.pdb"
Chain information for 6xt4_A_A_solenoid.pdb #8
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/7udo_A_A_solenoid.pdb"
Chain information for 7udo_A_A_solenoid.pdb #9
---
Chain | Description
A | No description available
27 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/8c3w_A_A_solenoid.pdb"
Chain information for 8c3w_A_A_solenoid.pdb #10
---
Chain | Description
A | No description available
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/8eov_A_A_solenoid.pdb"
Chain information for 8eov_A_A_solenoid.pdb #11
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/8erw_A_A_solenoid.pdb"
Chain information for 8erw_A_A_solenoid.pdb #12
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/8ga9_A_A_solenoid.pdb"
Chain information for 8ga9_A_A_solenoid.pdb #13
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/8k84_A_A_solenoid.pdb"
Chain information for 8k84_A_A_solenoid.pdb #14
---
Chain | Description
A | No description available
> open "/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from
> PDA/8ump_A_A_solenoid.pdb"
Chain information for 8ump_A_A_solenoid.pdb #15
---
Chain | Description
A | No description available
> set bgColor white
> ui tool show Matchmaker
> matchmaker #3,8,11-12,14-15#!2,4-7,9-10,13 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 3ltm_A_A_solenoid.pdb, chain A (#1) with 4pjs_A_A_solenoid.pdb,
chain A (#3), sequence alignment score = 128.4
RMSD between 16 pruned atom pairs is 0.688 angstroms; (across all 117 pairs:
12.275)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 6xt4_A_A_solenoid.pdb,
chain A (#8), sequence alignment score = 135.5
RMSD between 17 pruned atom pairs is 1.420 angstroms; (across all 110 pairs:
10.804)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8eov_A_A_solenoid.pdb,
chain A (#11), sequence alignment score = 98.4
RMSD between 14 pruned atom pairs is 0.850 angstroms; (across all 82 pairs:
13.869)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8erw_A_A_solenoid.pdb,
chain A (#12), sequence alignment score = 164.3
RMSD between 6 pruned atom pairs is 1.110 angstroms; (across all 119 pairs:
11.426)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8k84_A_A_solenoid.pdb,
chain A (#14), sequence alignment score = 108.3
RMSD between 8 pruned atom pairs is 1.276 angstroms; (across all 90 pairs:
15.171)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8ump_A_A_solenoid.pdb,
chain A (#15), sequence alignment score = 114.9
RMSD between 14 pruned atom pairs is 1.333 angstroms; (across all 80 pairs:
9.335)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 4gpm_A_A_solenoid.pdb,
chain A (#2), sequence alignment score = 71.5
RMSD between 16 pruned atom pairs is 0.997 angstroms; (across all 96 pairs:
14.746)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 4r5c_A_A_solenoid.pdb,
chain A (#4), sequence alignment score = 3.1
Fewer than 3 residues aligned; cannot match 3ltm_A_A_solenoid.pdb, chain A
with 4r5c_A_A_solenoid.pdb, chain A
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 5di5_A_A_solenoid.pdb,
chain A (#5), sequence alignment score = 10.1
Fewer than 3 residues aligned; cannot match 3ltm_A_A_solenoid.pdb, chain A
with 5di5_A_A_solenoid.pdb, chain A
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 5i9d_A_A_solenoid.pdb,
chain A (#6), sequence alignment score = 120.5
RMSD between 28 pruned atom pairs is 1.148 angstroms; (across all 119 pairs:
13.891)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 6veh_A_A_solenoid.pdb,
chain A (#7), sequence alignment score = 238.3
RMSD between 31 pruned atom pairs is 0.602 angstroms; (across all 77 pairs:
8.452)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 7udo_A_A_solenoid.pdb,
chain A (#9), sequence alignment score = 122.4
RMSD between 6 pruned atom pairs is 1.061 angstroms; (across all 106 pairs:
15.627)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8c3w_A_A_solenoid.pdb,
chain A (#10), sequence alignment score = 130.8
RMSD between 10 pruned atom pairs is 1.222 angstroms; (across all 113 pairs:
14.589)
Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8ga9_A_A_solenoid.pdb,
chain A (#13), sequence alignment score = 84.6
RMSD between 11 pruned atom pairs is 1.500 angstroms; (across all 93 pairs:
15.029)
> ui tool show Matchmaker
> matchmaker #3,8,11-12,14-15#!2,4-7,9-10,13 & sel to #1/A & sel pairing bs
No 'to' chains specified
> lighting gentle
> graphics silhouettes true
> hide #15 models
> hide #14 models
> hide #!13 models
> hide #12 models
> hide #11 models
> hide #!10 models
> hide #!9 models
> hide #8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #3 models
> hide #!2 models
> show #!2 models
> show #3 models
> show #!4 models
> hide #!4 models
> hide #3 models
> hide #!2 models
> hide #1 target a
> color #1 #fd5901ff
> show #!2 models
> hide #!1 models
> color #2 #fd5901ff
> show #3 models
> hide #!2 models
> color #3 #fd5901ff
> show #!4 models
> hide #3 models
> color #4 #ff8500ff
> show #3 models
> hide #3 models
> show #!5 models
> hide #!4 models
> color #5 #faab36ff
> show #!6 models
> hide #!5 models
> color #6 #fd5901ff
> show #!7 models
> hide #!6 models
> color #7 #fd5901ff
> show #8 models
> hide #!7 models
> color #8 #fd5901ff
> show #!9 models
> hide #8 models
> color #9 #fd5901ff
> show #!10 models
> hide #!9 models
> color #10 #fd5901ff
> show #11 models
> hide #!10 models
> color #11 #fd5901ff
> show #12 models
> hide #11 models
> color #12 #fd5901ff
> show #!13 models
> hide #12 models
> color #13 #fd5901ff
> show #14 models
> hide #!13 models
> color #14 #fd5901ff
> show #15 models
> hide #14 models
> color #15 #fd5901ff
> hide #15 models
> show #!1 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/3ltm.png
> transparentBackground true width 3000 height 3000
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/4gpm.png
> transparentBackground true width 3000 height 3000
> show #3 models
> hide #!2 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/4pjs.png
> transparentBackground true width 3000 height 3000
> show #!4 models
> hide #3 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/4r5c.png
> transparentBackground true width 3000 height 3000
> show #!5 models
> hide #!4 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5di5.png
> transparentBackground true width 3000 height 3000
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> open 5di5
Summary of feedback from opening 5di5 fetched from pdb
---
note | Fetching compressed mmCIF 5di5 from http://files.rcsb.org/download/5di5.cif
5di5 title:
beta1 t801 loop variant in P3221 [more info...]
Chain information for 5di5 #16
---
Chain | Description
A | beta1 t801 loop variant
5di5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> select add #16
1388 atoms, 1379 bonds, 210 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open 5i9d
Summary of feedback from opening 5i9d fetched from pdb
---
note | Fetching compressed mmCIF 5i9d from http://files.rcsb.org/download/5i9d.cif
5i9d title:
Crystal structure of designed pentatricopeptide repeat protein dPPR-U8A2 in
complex with its target RNA U8A2 [more info...]
Chain information for 5i9d #16
---
Chain | Description
A | pentatricopeptide repeat protein dPPR-U8A2
B | RNA (5'-R(*GP*GP*GP*G*UP*UP*UP*UP*AP*AP*UP*UP*UP*UP*CP*CP*CP*C)-3')
> select nucleic-acid
198 atoms, 218 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color #16 #fd5901ff
> ui tool show "Side View"
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5i9d.png
> transparentBackground true width 3000 height 3000
> hide #!16 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/6veh.png
> transparentBackground true width 3000 height 3000
> show #8 models
> hide #!7 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/6xt4.png
> transparentBackground true width 3000 height 3000
> show #!9 models
> hide #8 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/7udo.png
> transparentBackground true width 3000 height 3000
> show #!10 models
> hide #!9 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8c3w.png
> transparentBackground true width 3000 height 3000
> show #11 models
> hide #!10 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8eov.png
> transparentBackground true width 3000 height 3000
> show #12 models
> hide #11 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8erw.png
> transparentBackground true width 3000 height 3000
> show #!13 models
> hide #12 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8ga9.png
> transparentBackground true width 3000 height 3000
> show #14 models
> hide #!13 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8k84.png
> transparentBackground true width 3000 height 3000
> show #15 models
> hide #14 models
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8ump.png
> transparentBackground true width 3000 height 3000
> show #!16 models
> hide #15 models
> hide #!16 models
> open /Users/georginikov/Downloads/5DN0.cxs
opened ChimeraX session
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0.png
> transparentBackground true width 3000 height 3000
> transparency /A 50 cartoons
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0_50.png
> transparentBackground true width 3000 height 3000
> lighting gentle
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0_50.png
> transparentBackground true width 3000 height 3000
> ui tool show "Side View"
> save
> /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0_50.png
> transparentBackground true width 3000 height 3000
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/georginikov/Downloads/All_pdbs_colored_plddt_GA_plot.cxs
Log from Mon Oct 7 10:50:42 2024 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/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_96/Sequence_1/1Sequence_1_unrelaxed_rank_1_model_5.pdb
Chain information for 1Sequence_1_unrelaxed_rank_1_model_5.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_101/Sequence_1/2_newSequence_1_unrelaxed_rank_1_model_2.pdb
Chain information for 2_newSequence_1_unrelaxed_rank_1_model_2.pdb #2
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_112/Sequence_1/3newSequence_1_unrelaxed_rank_1_model_3.pdb
Chain information for 3newSequence_1_unrelaxed_rank_1_model_3.pdb #3
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_122/Sequence_1/4Sequence_1_unrelaxed_rank_1_model_5.pdb
Chain information for 4Sequence_1_unrelaxed_rank_1_model_5.pdb #4
---
Chain | Description
A | No description available
> colorConfidence truecartoon
Unknown command: colorConfidence truecartoon
> color bfactor palette alphafold
5244 atoms, 600 residues, atom bfactor range 20.2 to 97.3
> set bgColor white
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_332/Sequence_1/1Sequence_1_unrelaxed_rank_1_model_3.pdb
Chain information for 1Sequence_1_unrelaxed_rank_1_model_3.pdb #5
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_337/Sequence_1/2newSequence_1_unrelaxed_rank_1_model_4.pdb
Chain information for 2newSequence_1_unrelaxed_rank_1_model_4.pdb #6
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_355/Sequence_1/3new_Sequence_1_unrelaxed_rank_1_model_4.pdb
Chain information for 3new_Sequence_1_unrelaxed_rank_1_model_4.pdb #7
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_372/Sequence_1/4newSequence_1_unrelaxed_rank_1_model_2.pdb
Chain information for 4newSequence_1_unrelaxed_rank_1_model_2.pdb #8
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_404/Sequence_1/5Sequence_1_unrelaxed_rank_1_model_4.pdb
Chain information for 5Sequence_1_unrelaxed_rank_1_model_4.pdb #9
---
Chain | Description
A | No description available
> color bfactor palette alphafold
11172 atoms, 1290 residues, atom bfactor range 20.2 to 97.3
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_68/Sequence_1/1Sequence_1_unrelaxed_rank_1_model_2.pdb
Chain information for 1Sequence_1_unrelaxed_rank_1_model_2.pdb #10
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_102/Sequence_1/2newSequence_1_unrelaxed_rank_1_model_2.pdb
Chain information for 2newSequence_1_unrelaxed_rank_1_model_2.pdb #11
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_108/Sequence_1/3Sequence_1_unrelaxed_rank_1_model_2.pdb
Chain information for 3Sequence_1_unrelaxed_rank_1_model_2.pdb #12
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_130/Sequence_1/4Sequence_1_unrelaxed_rank_1_model_4.pdb
Chain information for 4Sequence_1_unrelaxed_rank_1_model_4.pdb #13
---
Chain | Description
A | No description available
> open
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_155/Sequence_1/5Sequence_1_unrelaxed_rank_1_model_3.pdb
Chain information for 5Sequence_1_unrelaxed_rank_1_model_3.pdb #14
---
Chain | Description
A | No description available
> color bfactor palette alphafold
17600 atoms, 2050 residues, atom bfactor range 20.2 to 97.3
> graphics silhouettes true
> save
> /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/All_pdbs_colored_plddt_GA_plot.cxs
\u2014\u2014\u2014 End of log from Mon Oct 7 10:50:42 2024 \u2014\u2014\u2014
opened ChimeraX session
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
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 Air
Model Identifier: MacBookAir10,1
Model Number: Z1240001TB/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 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: 34 days, 13 hours, 39 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 13 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 , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties.