![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15947 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-12.7-x86_64-i386-64bit
ChimeraX Version: 1.8rc202406042103 (2024-06-04 21:03:50 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 0x000000010ec0e600 (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 307 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, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 59)
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{
"uptime" : 220000,
"procLaunch" : "2024-09-13 09:13:49.0417 +0800",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro13,3",
"procStartAbsTime" : 209629280582645,
"coalitionID" : 10881,
"osVersion" : {
"train" : "macOS 12.7",
"build" : "21G816",
"releaseType" : "User"
},
"captureTime" : "2024-09-13 12:46:36.3905 +0800",
"incident" : "88641950-57AE-46ED-B0C3-E81777DA7394",
"bug_type" : "309",
"pid" : 94361,
"procExitAbsTime" : 221084496634718,
"cpuType" : "X86-64",
"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":"6317AAE8-C86F-5FE7-BCDC-43038A717320","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DB767E10-B824-ED52-901F-50AB21D12C28",
"wakeTime" : 2536,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "B1B2722D-D1DD-47BF-B5B4-CB374446617F",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4356059136\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103a43000-103a47000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4356059136\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103a43000-103a47000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"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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"uuid" : "e20a0ae9-767a-313b-b0ca-5ebeb955f449",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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"arch" : "x86_64",
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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{
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"base" : 4690751488,
"size" : 655360,
"uuid" : "a9df58b1-89b1-36c8-9d9e-fe251bf025f2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
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"size" : 5373952,
"uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4666228736,
"size" : 2867200,
"uuid" : "04d3e498-8e36-3f03-9aa5-8a19040cc57f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
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"arch" : "x86_64",
"base" : 4356059136,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
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"uuid" : "65540238-1367-3f2e-978b-3278e73c124b",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"arch" : "x86_64",
"base" : 140703401062400,
"size" : 364544,
"uuid" : "a372724f-4642-369b-a01b-28e1f5e83ff1",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
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"size" : 7274496,
"uuid" : "57e18c1d-e3ae-37c5-ada4-dcc62718794e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
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"uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
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"size" : 19331678208,
"uuid" : "78895403-2898-3ade-a242-28aea75636b5"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 2040K 50 \nColorSync 232K 28 \nCoreAnimation 3688K 97 \nCoreGraphics 16K 3 \nCoreImage 12K 1 \nCoreServices 624K 2 \nCoreUI image data 5184K 38 \nFoundation 44K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 2.2G 1358 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 140K 35 \nStack 160.8M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 393.7M 319 \n__CTF 756 1 \n__DATA 52.2M 714 \n__DATA_CONST 42.4M 408 \n__DATA_DIRTY 1796K 233 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.0M 159 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 875.7M 714 \n__UNICODE 592K 1 \ndyld private memory 1056K 3 \nmapped file 548.8M 93 \nshared memory 3496K 26 \n=========== ======= ======= \nTOTAL 5.0G 4356 \nTOTAL, minus reserved VM space 5.0G 4356 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406042103 (2024-06-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sunfh/Desktop/ARP/01_maps&models/3_ncBAF-NCP-
> Apo/J1462_J1431_zflip_3.11Amap.mrc
Opened J1462_J1431_zflip_3.11Amap.mrc as #1, grid size 432,432,432, pixel
0.93, shown at level 0.039, step 2, values float32
> volume #1 level 0.07147
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> set bgColor white
> open /Users/sunfh/Desktop/ARP/01_maps&models/3_ncBAF-NCP-Apo/ncBAF-NCP-
> apo.pdb
Chain information for ncBAF-NCP-apo.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
> hide atoms
> show cartoons
> hide #!2 models
> transparency 50
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> color bychain
> show #!1 models
> open
> /Users/sunfh/Desktop/ARP/01_maps&models/1_ARPapo(ATP)/ARPapo_lastframe_rsr38_ATPadd-
> coot-1.pdb
Chain information for ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open /Users/sunfh/Desktop/ARP/01_maps&models/4_ncBAF-NCP-
> BeFx/cryosparc_P12_J2398_006_volume_map_Zflip.mrc
Opened cryosparc_P12_J2398_006_volume_map_Zflip.mrc as #4, grid size
192,192,192, pixel 1.46, shown at level 0.11, step 1, values float32
> open /Users/sunfh/Desktop/ARP/01_maps&models/4_ncBAF-NCP-
> BeFx/lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc
Opened lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc as #5, grid size
256,256,256, pixel 1.46, shown at level 0.087, step 1, values float32
> surface dust #1 size 9.3
> surface dust #4 size 14.6
> surface dust #5 size 14.6
> volume #1 step 1
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> volume #1 level 0.08597
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 76 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #1 level 0.09
> volume #1 level 0.07
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-8.322,0,1,0,156.47,0,0,1,100.8
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.17141,-0.97607,0.13382,266.21,-0.48238,-0.035286,-0.87525,489.99,0.85903,-0.21458,-0.46479,223.35
> view matrix models
> #4,-0.67733,-0.68094,-0.27847,347.17,-0.39476,0.016992,0.91863,221.45,-0.6208,0.73214,-0.28032,254.72
> view matrix models
> #4,-0.35069,-0.88851,-0.29592,336.81,-0.93483,0.31335,0.16703,353.91,-0.055679,0.33521,-0.9405,329.88
> view matrix models
> #4,-0.72825,0.67297,0.12945,102.47,0.61639,0.72578,-0.30547,157.95,-0.29952,-0.14267,-0.94336,430.78
> view matrix models
> #4,-0.74322,0.64135,0.19053,100.47,0.51464,0.72999,-0.44973,190.69,-0.42752,-0.2362,-0.8726,451.08
> view matrix models
> #4,-0.70625,0.70334,0.080814,102,0.68571,0.70797,-0.16905,132.48,-0.17611,-0.063976,-0.98229,408.78
> view matrix models
> #4,-0.74042,0.64917,0.17424,101.25,0.54315,0.73058,-0.41381,181.89,-0.39593,-0.21176,-0.89353,446.36
> view matrix models
> #4,-0.70133,0.70915,0.072442,101.69,0.69634,0.70329,-0.14316,128.16,-0.15247,-0.049955,-0.98705,404.34
> view matrix models
> #4,-0.68386,0.7281,0.046988,100.23,0.72573,0.68544,-0.059033,115.19,-0.075189,-0.006269,-0.99715,389.39
> view matrix models
> #4,-0.98369,0.17945,0.012228,223.04,0.17828,0.96368,0.19885,110.76,0.0239,0.19779,-0.97995,344.74
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.98369,0.17945,0.012228,248.99,0.17828,0.96368,0.19885,-2.4228,0.0239,0.19779,-0.97995,332.9
> select subtract #4
Nothing selected
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.90388,-0.30807,-0.2968,351.64,-0.42557,0.71802,0.55077,62.719,0.043436,0.62414,-0.78011,241.27
> view matrix models
> #4,-0.85929,-0.50613,-0.073862,343.27,-0.4417,0.66143,0.60615,65.25,-0.25793,0.55348,-0.79192,292.39
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.85929,-0.50613,-0.073862,396.7,-0.4417,0.66143,0.60615,77.284,-0.25793,0.55348,-0.79192,275.97
> fitmap #4 inMap #1
Fit map cryosparc_P12_J2398_006_volume_map_Zflip.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 70696 points
correlation = 0.6215, correlation about mean = 0.2437, overlap = 1377
steps = 224, shift = 9.51, angle = 22.8 degrees
Position of cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.91917921 -0.30346143 0.25103933 334.91516629
-0.07949987 0.76725943 0.63639040 18.04608299
-0.38573223 0.56499923 -0.72937406 285.28519424
Axis -0.10517672 0.93812080 0.32995035
Axis point 192.72821386 0.00000000 107.50839520
Rotation angle (degrees) 160.16048324
Shift along axis 75.83407713
> select subtract #4
Nothing selected
> view #4 clip false
> volume #1 level 0.1316
> volume #4 level 0.2464
> select add #4
2 models selected
> view matrix models
> #4,-0.91918,-0.30346,0.25104,334.41,-0.0795,0.76726,0.63639,17.28,-0.38573,0.565,-0.72937,286.95
> view matrix models
> #4,-0.91918,-0.30346,0.25104,334.57,-0.0795,0.76726,0.63639,17.719,-0.38573,0.565,-0.72937,286.31
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.90694,-0.24803,0.34049,312.67,-0.086624,0.90081,0.42548,28.314,-0.41225,0.35639,-0.83847,334.92
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.90694,-0.24803,0.34049,313.67,-0.086624,0.90081,0.42548,23.657,-0.41225,0.35639,-0.83847,334.93
> fitmap #4 inMap #1
Fit map cryosparc_P12_J2398_006_volume_map_Zflip.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 22550 points
correlation = 0.949, correlation about mean = 0.7368, overlap = 2049
steps = 92, shift = 2.85, angle = 4.91 degrees
Position of cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.91221276 -0.21401087 0.34938121 310.20640578
-0.08636231 0.93401504 0.34663734 30.06097252
-0.40051147 0.28603364 -0.87050291 345.29366974
Axis -0.07941884 0.98270572 0.16727857
Axis point 190.09389174 0.00000000 138.29241227
Rotation angle (degrees) 157.57059069
Shift along axis 62.66508749
> volume #1 level 0.07
> volume #4 level 0.1
> select subtract #4
Nothing selected
> volume #4 level 0.14
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> volume #1 color #b2b2b2
> volume #1 level 0.075
> hide #!4 models
> show #!5 models
> select add #5
2 models selected
> view matrix models #5,1,0,0,-23.541,0,1,0,22.524,0,0,1,138.28
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.63119,0.66329,-0.40204,-11.17,0.54841,-0.015106,0.83607,-36.075,0.54849,-0.74821,-0.37329,452.53
> view matrix models
> #5,0.89174,0.2277,-0.39108,26.172,0.12797,0.70204,0.70055,-76.446,0.43407,-0.67476,0.5969,271.59
> view matrix models
> #5,0.94063,0.13651,-0.31076,19.972,0.05854,0.8366,0.54468,-60.586,0.33434,-0.53054,0.77894,225.87
> hide #!1 models
> show #!4 models
> hide #!4 models
> transparency sel 50
> show #!4 models
> view matrix models
> #5,0.92858,0.15954,-0.3351,22.264,0.075114,0.80342,0.59066,-65.852,0.36346,-0.57364,0.73405,237.83
> select subtract #5
Nothing selected
> select add #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.92858,0.15954,-0.3351,46.492,0.075114,0.80342,0.59066,-41.96,0.36346,-0.57364,0.73405,120.5
> select subtract #5
Nothing selected
> ui mousemode right "rotate selected models"
> select add #5
2 models selected
> view matrix models
> #5,0.95129,0.019827,0.30766,-53.74,-0.099356,-0.92497,0.36682,377.33,0.29185,-0.37952,-0.87795,405.68
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95129,0.019827,0.30766,-49.32,-0.099356,-0.92497,0.36682,309.08,0.29185,-0.37952,-0.87795,388.73
> fitmap #5 inMap #4
Fit map lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc in map
cryosparc_P12_J2398_006_volume_map_Zflip.mrc using 167743 points
correlation = 0.7285, correlation about mean = 0.4015, overlap = 2659
steps = 120, shift = 11, angle = 14 degrees
Position of lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) relative to
cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) coordinates:
Matrix rotation and translation
-0.99929026 -0.01783823 -0.03317807 338.15099837
0.01671528 -0.99928813 0.03382087 308.80044221
-0.03375776 0.03324229 0.99887705 -52.84408272
Axis -0.01673993 0.01677171 0.99971920
Axis point 167.29459142 156.30109881 0.00000000
Rotation angle (degrees) 179.00978766
Shift along axis -53.31075656
> fitmap #5 inMap #4
Fit map lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc in map
cryosparc_P12_J2398_006_volume_map_Zflip.mrc using 167743 points
correlation = 0.7284, correlation about mean = 0.4014, overlap = 2659
steps = 28, shift = 0.022, angle = 0.0266 degrees
Position of lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) relative to
cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) coordinates:
Matrix rotation and translation
-0.99927401 -0.01819845 -0.03347030 338.25054458
0.01706540 -0.99928183 0.03383209 308.73005867
-0.03406196 0.03323635 0.99886693 -52.78133215
Axis -0.01688918 0.01677312 0.99971667
Axis point 167.31373254 156.29580092 0.00000000
Rotation angle (degrees) 178.98942666
Shift along axis -53.30078544
> volume #5 level 0.1067
> fitmap #5 inMap #4
Fit map lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc in map
cryosparc_P12_J2398_006_volume_map_Zflip.mrc using 122461 points
correlation = 0.7403, correlation about mean = 0.3477, overlap = 2392
steps = 60, shift = 0.169, angle = 0.0816 degrees
Position of lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) relative to
cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) coordinates:
Matrix rotation and translation
-0.99929020 -0.01788361 -0.03315542 338.02548505
0.01671576 -0.99924147 0.03517221 308.49776657
-0.03375928 0.03459302 0.99883114 -53.21016163
Axis -0.01673484 0.01744767 0.99970772
Axis point 167.22823449 156.17224125 0.00000000
Rotation angle (degrees) 179.00846178
Shift along axis -53.46884379
> fitmap #5 inMap #4
Fit map lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc in map
cryosparc_P12_J2398_006_volume_map_Zflip.mrc using 122461 points
correlation = 0.7403, correlation about mean = 0.3478, overlap = 2392
steps = 40, shift = 0.00536, angle = 0.00569 degrees
Position of lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) relative to
cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) coordinates:
Matrix rotation and translation
-0.99928653 -0.01794811 -0.03323084 338.05576282
0.01677759 -0.99924038 0.03517381 308.48360561
-0.03383690 0.03459118 0.99882857 -53.19679482
Axis -0.01677313 0.01744763 0.99970708
Axis point 167.23763536 156.17049618 0.00000000
Rotation angle (degrees) 179.00484027
Shift along axis -53.46915815
> select subtract #5
Nothing selected
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> select add #3
6740 atoms, 6888 bonds, 2 pseudobonds, 849 residues, 2 models selected
> view matrix models #3,1,0,0,5.3423,0,1,0,-12.281,0,0,1,28.873
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.14589,-0.93398,0.3262,207.85,0.96081,0.055197,-0.27167,23.955,0.23573,0.35305,0.90542,-39.627
> select subtract #3
Nothing selected
> hide #!5 models
> color #!3 bychain
> show #!5 models
> select add #3
6740 atoms, 6888 bonds, 2 pseudobonds, 849 residues, 2 models selected
> view matrix models
> #3,0.64753,-0.31152,-0.69546,197.16,-0.57107,-0.80264,-0.17219,342.78,-0.50456,0.50865,-0.69763,270.89
> view matrix models
> #3,-0.71706,-0.46528,-0.51898,383.69,-0.67041,0.25667,0.69618,85.25,-0.19071,0.84714,-0.49597,151.22
> view matrix models
> #3,-0.43029,-0.88094,-0.19697,355.55,-0.77558,0.47244,-0.41867,229.09,0.46188,-0.027381,-0.88652,237.64
> view matrix models
> #3,0.10985,-0.63073,0.76819,107.57,-0.7243,-0.58007,-0.3727,361.82,0.68068,-0.51545,-0.52056,222.77
> view matrix models
> #3,0.18824,-0.89872,0.39607,187.06,-0.52984,0.24663,0.81144,50.58,-0.82694,-0.3626,-0.42975,398.83
> view matrix models
> #3,-0.56104,-0.21647,0.79899,139.11,-0.15044,0.97579,0.15874,-10.594,-0.81401,-0.031145,-0.58002,372.36
> view matrix models
> #3,-0.58578,-0.029502,0.80993,114.99,-0.19136,0.97612,-0.10284,32.42,-0.78755,-0.21523,-0.57744,393.92
> select subtract #3
Nothing selected
> select add #3
6740 atoms, 6888 bonds, 2 pseudobonds, 849 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.58578,-0.029502,0.80993,114.45,-0.19136,0.97612,-0.10284,100.26,-0.78755,-0.21523,-0.57744,368
> select subtract #3
Nothing selected
> select add #3
6740 atoms, 6888 bonds, 2 pseudobonds, 849 residues, 2 models selected
> view matrix models
> #3,-0.58578,-0.029502,0.80993,132.46,-0.19136,0.97612,-0.10284,47.049,-0.78755,-0.21523,-0.57744,437.22
> select subtract #3
Nothing selected
> select add #3
6740 atoms, 6888 bonds, 2 pseudobonds, 849 residues, 2 models selected
> view matrix models
> #3,-0.58578,-0.029502,0.80993,171.63,-0.19136,0.97612,-0.10284,37.714,-0.78755,-0.21523,-0.57744,400.18
> select subtract #3
Nothing selected
> select add #3
6740 atoms, 6888 bonds, 2 pseudobonds, 849 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.36685,-0.1821,0.91228,45.371,0.056512,0.9832,0.17354,-37.311,-0.92856,-0.012108,0.37098,256.16
> view matrix models
> #3,0.49958,-0.38318,0.77691,74.164,-0.38375,0.70615,0.59505,2.46,-0.77663,-0.59542,0.20574,339.73
> view matrix models
> #3,-0.25965,-0.57049,0.77918,205.8,-0.69231,0.67249,0.26167,97.787,-0.67327,-0.4715,-0.56956,418.77
> view matrix models
> #3,-0.32197,-0.26174,0.90985,152.88,-0.66702,0.74472,-0.021798,124.69,-0.67188,-0.61391,-0.41436,416.23
> view matrix models
> #3,-0.29041,-0.4612,0.83842,186.43,-0.68583,0.71134,0.15374,106.89,-0.66731,-0.53036,-0.52288,419.47
> view matrix models
> #3,0.0431,-0.48813,0.87171,138.9,-0.99901,-0.030775,0.032161,271.19,0.011128,-0.87223,-0.48897,367.56
> view matrix models
> #3,-0.20656,-0.23808,0.94903,127.9,-0.97712,-1.7957e-05,-0.21268,298.82,0.050653,-0.97124,-0.23263,339.22
> fitmap #3 inMap #5
Fit molecule ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb (#3) to map
lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) using 6740 atoms
average map value = 0.08871, steps = 128
shifted from previous position = 19.1
rotated from previous position = 16.7 degrees
atoms outside contour = 4868, contour level = 0.10669
Position of ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb (#3) relative to
lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.07367878 -0.72476282 0.68504765 197.79035535
0.93961318 0.17975279 0.29123185 56.18452714
-0.33421325 0.66513741 0.66775274 42.88842395
Axis 0.18815980 0.51292077 0.83756085
Axis point 92.00524316 110.13567642 0.00000000
Rotation angle (degrees) 96.49327688
Shift along axis 101.95606976
> volume #5 level 0.07195
> fitmap #3 inMap #5
Fit molecule ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb (#3) to map
lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) using 6740 atoms
average map value = 0.08871, steps = 44
shifted from previous position = 0.0283
rotated from previous position = 0.0268 degrees
atoms outside contour = 1810, contour level = 0.071955
Position of ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb (#3) relative to
lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.07408333 -0.72469719 0.68507345 197.82919891
0.93951144 0.17964072 0.29162897 56.18559718
-0.33440978 0.66523919 0.66755292 42.92442018
Axis 0.18801891 0.51305374 0.83751104
Axis point 92.03545386 110.11892323 0.00000000
Rotation angle (degrees) 96.51393441
Shift along axis 101.97153671
> fitmap #3 inMap #5
Fit molecule ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb (#3) to map
lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) using 6740 atoms
average map value = 0.08871, steps = 40
shifted from previous position = 0.0308
rotated from previous position = 0.0306 degrees
atoms outside contour = 1811, contour level = 0.071955
Position of ARPapo_lastframe_rsr38_ATPadd-coot-1.pdb (#3) relative to
lowpass30A_cryosparc_P12_J2599_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.07359840 -0.72475102 0.68506878 197.77508311
0.93961621 0.17981979 0.29118073 56.17969236
-0.33422245 0.66513217 0.66775336 42.89124476
Axis 0.18818129 0.51293169 0.83754933
Axis point 92.00003666 110.13093313 0.00000000
Rotation angle (degrees) 96.48900972
Shift along axis 101.95744871
> select subtract #3
Nothing selected
> show #!2 models
> open /Users/sunfh/Desktop/ARP/01_maps&models/5_ncBAF_delN-NCP-
> BeFx/cryosparc_P12_J2627_006_volume_map.mrc
Opened cryosparc_P12_J2627_006_volume_map.mrc as #6, grid size 384,384,384,
pixel 0.73, shown at level 0.0388, step 2, values float32
> hide #!3 models
> hide #!2 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> surface dust #6 size 7.3
> show #!1 models
> select add #6
2 models selected
> view matrix models
> #6,0.83302,-0.10334,0.54351,-40.163,-0.012238,-0.9856,-0.16864,318.14,0.55311,0.13383,-0.82229,166.88
> view matrix models
> #6,-0.48419,-0.8693,0.099406,309.14,-0.8744,0.47667,-0.090632,205.01,0.031402,-0.1308,-0.99091,298.48
> view matrix models
> #6,-0.87072,-0.04798,0.48942,183.47,-0.074614,0.9966,-0.035045,15.303,-0.48608,-0.067032,-0.87134,340.14
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.87072,-0.04798,0.48942,250.46,-0.074614,0.9966,-0.035045,42.4,-0.48608,-0.067032,-0.87134,419.07
> hide #!6 models
> transparency #1.1 50
> show #!6 models
> select subtract #6
Nothing selected
> select add #6
2 models selected
> view matrix models
> #6,-0.87072,-0.04798,0.48942,253.82,-0.074614,0.9966,-0.035045,65.317,-0.48608,-0.067032,-0.87134,404.41
> fitmap #6 inMap #1
Fit map cryosparc_P12_J2627_006_volume_map.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 70717 points
correlation = 0.684, correlation about mean = 0.2634, overlap = 486.3
steps = 224, shift = 14.7, angle = 9.62 degrees
Position of cryosparc_P12_J2627_006_volume_map.mrc (#6) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.91052563 -0.13891191 0.38941822 298.45364732
-0.18435027 0.97946313 -0.08165144 87.23965733
-0.37007843 -0.14613508 -0.91743473 415.07948169
Axis -0.08444885 0.99464935 -0.05950683
Axis point 194.54868669 0.00000000 180.07139645
Rotation angle (degrees) 157.55532457
Shift along axis 36.86873743
> select subtract #6
Nothing selected
> volume #6 level 0.05876
> volume #6 step 1
> volume #6 level 0.06865
> view #6 clip false
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.92797,-0.22301,0.29855,325.87,-0.15559,0.95986,0.23338,42.114,-0.33861,0.17012,-0.92542,365.55
> fitmap #6 inMap #1
Fit map cryosparc_P12_J2627_006_volume_map.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 246333 points
correlation = 0.9349, correlation about mean = 0.7436, overlap = 5371
steps = 80, shift = 5.5, angle = 3.51 degrees
Position of cryosparc_P12_J2627_006_volume_map.mrc (#6) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.90672916 -0.27012095 0.32384704 324.06052698
-0.18684967 0.94577133 0.26571374 49.12000777
-0.37806009 0.18041969 -0.90803045 366.41825699
Axis -0.11980225 0.98588413 0.11696111
Axis point 198.63828959 0.00000000 149.46577496
Rotation angle (degrees) 159.14657288
Shift along axis 52.46014146
> select subtract #6
Nothing selected
> volume #1 color #b2b2b2
> show #!4 models
> volume #4 color #ffffb29b
> hide #!1 models
> volume #4 level 0.1683
> volume #6 level 0.05665
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #1 level 0.07
> volume #1 level 0.075
> volume #1 color #b2b2b286
> volume #1 color #b2b2b2a7
> volume #1 color #b2b2b280
> volume #4 color #ffffb2
> volume #4 color #ffffb285
> volume #6 color #b2b2ff7f
> volume #6 color #b2b2ff
> volume #4 color #ffffb2
> volume #1 color #b2b2b2
> volume #1 level 0.1185
> volume #6 level 0.1117
> volume #1 color #b2b2b27f
> volume #1 color #b2b2b2ae
> volume #1 color #b2b2b2d1
> volume #6 level 0.1145
> volume #4 level 0.331
> volume #1 color #b2b2b2bf
> volume #1 color #b2b2b2a6
> volume #1 level 0.1529
> volume #6 color #b2b2ffa6
> volume #6 color #b2b2ff
> select add #6
2 models selected
> fitmap #6 inMap #1
Fit map cryosparc_P12_J2627_006_volume_map.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 76139 points
correlation = 0.9732, correlation about mean = 0.6114, overlap = 3232
steps = 44, shift = 0.0292, angle = 0.111 degrees
Position of cryosparc_P12_J2627_006_volume_map.mrc (#6) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.90705473 -0.27102483 0.32217582 324.42861703
-0.18793674 0.94541918 0.26619985 49.27943453
-0.37673797 0.18090916 -0.90848246 366.23002252
Axis -0.12029985 0.98579598 0.11719313
Axis point 198.67881573 0.00000000 149.45434616
Rotation angle (degrees) 159.23767983
Shift along axis 52.47040025
> fitmap #6 inMap #1
Fit map cryosparc_P12_J2627_006_volume_map.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 76139 points
correlation = 0.9732, correlation about mean = 0.6112, overlap = 3232
steps = 44, shift = 0.0157, angle = 0.0169 degrees
Position of cryosparc_P12_J2627_006_volume_map.mrc (#6) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.90702070 -0.27104260 0.32225668 324.42395794
-0.18804420 0.94546954 0.26594498 49.31138441
-0.37676629 0.18061910 -0.90852843 366.27103938
Axis -0.12033227 0.98580904 0.11704991
Axis point 198.68866582 0.00000000 149.47284476
Rotation angle (degrees) 159.23457459
Shift along axis 52.44493019
> fitmap #6 inMap #1
Fit map cryosparc_P12_J2627_006_volume_map.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 76139 points
correlation = 0.9731, correlation about mean = 0.6112, overlap = 3232
steps = 44, shift = 0.00308, angle = 0.0014 degrees
Position of cryosparc_P12_J2627_006_volume_map.mrc (#6) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.90702058 -0.27104885 0.32225175 324.42744610
-0.18804205 0.94546340 0.26596833 49.30770729
-0.37676765 0.18064187 -0.90852334 366.26531553
Axis -0.12033351 0.98580743 0.11706217
Axis point 198.68956777 0.00000000 149.46963171
Rotation angle (degrees) 159.23465003
Shift along axis 52.44422141
> select subtract #6
Nothing selected
> select add #4
2 models selected
> show #!4 models
> hide #!6 models
> fitmap #4 inMap #1
Fit map cryosparc_P12_J2398_006_volume_map_Zflip.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 12852 points
correlation = 0.9672, correlation about mean = 0.6921, overlap = 1656
steps = 44, shift = 0.0221, angle = 0.0655 degrees
Position of cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.91247076 -0.21446781 0.34842600 310.41387725
-0.08717174 0.93395640 0.34659275 30.20336749
-0.39974768 0.28588285 -0.87090343 345.25541557
Axis -0.07973980 0.98269347 0.16719784
Axis point 190.12230704 0.00000000 138.31756436
Rotation angle (degrees) 157.62449963
Shift along axis 62.65426863
> fitmap #4 inMap #1
Fit map cryosparc_P12_J2398_006_volume_map_Zflip.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 12852 points
correlation = 0.9672, correlation about mean = 0.6922, overlap = 1656
steps = 44, shift = 0.00207, angle = 0.0128 degrees
Position of cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.91248806 -0.21457329 0.34831572 310.44446090
-0.08723065 0.93388126 0.34678035 30.19693332
-0.39969532 0.28604912 -0.87087287 345.21963523
Axis -0.07978357 0.98267388 0.16729203
Axis point 190.12725769 0.00000000 138.30148656
Rotation angle (degrees) 157.62915707
Shift along axis 62.65786347
> fitmap #4 inMap #1
Fit map cryosparc_P12_J2398_006_volume_map_Zflip.mrc in map
J1462_J1431_zflip_3.11Amap.mrc using 12852 points
correlation = 0.9672, correlation about mean = 0.692, overlap = 1656
steps = 40, shift = 0.0195, angle = 0.00408 degrees
Position of cryosparc_P12_J2398_006_volume_map_Zflip.mrc (#4) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
-0.91248042 -0.21461546 0.34830976 310.45942591
-0.08729171 0.93388842 0.34674570 30.19928561
-0.39969943 0.28599411 -0.87088905 345.21571831
Axis -0.07981067 0.98267578 0.16726794
Axis point 190.13505468 0.00000000 138.29836924
Rotation angle (degrees) 157.62926105
Shift along axis 62.64165326
> show #!6 models
> select subtract #4
Nothing selected
> volume #4 level 0.34
> volume #6 level 0.118
> volume #1 level 0.158
> view #6 clip false
> volume #1 color #b2b2b2
> volume #1 color #b2b2b27e
> volume #1 color #b2b2b2d0
> volume #1 color #b2b2b29c
> volume #1 level 0.065
> volume #4 level 0.2032
> volume #6 level 0.05942
> volume #1 color #b2b2b2
> volume #1 level 0.07
> volume #6 level 0.06224
> volume #4 level 0.2056
> volume #1 level 0.1008
> volume #1 level 0.1189
> volume #1 level 0.0845
> open /Users/sunfh/Desktop/ARP/01_maps&models/3_ncBAF-NCP-
> Apo/NUC_local_map/J1443_3.05Alocalref_map.mrc
Opened J1443_3.05Alocalref_map.mrc as #7, grid size 432,432,432, pixel 0.93,
shown at level 0.0348, step 2, values float32
> hide #!4 models
> hide #!1 models
> volume #7 level 0.07512
> surface dust #7 size 9.3
> volume #7 step 1
> volume #7 level 0.07512
> volume #7 level 0.08464
> show #!1 models
> select add #7
2 models selected
> fitmap #7 inMap #1
Fit map J1443_3.05Alocalref_map.mrc in map J1462_J1431_zflip_3.11Amap.mrc
using 148709 points
correlation = 0.9922, correlation about mean = 0.9622, overlap = 6984
steps = 52, shift = 0.748, angle = 0.0367 degrees
Position of J1443_3.05Alocalref_map.mrc (#7) relative to
J1462_J1431_zflip_3.11Amap.mrc (#1) coordinates:
Matrix rotation and translation
0.99999981 0.00006548 -0.00061044 0.06830846
-0.00006560 0.99999998 -0.00018225 -0.00347744
0.00061043 0.00018229 0.99999980 -0.89806034
Axis 0.28460268 -0.95316752 -0.10233768
Axis point 1451.99866823 0.00000000 57.99450423
Rotation angle (degrees) 0.03669364
Shift along axis 0.11466077
> select subtract #7
Nothing selected
> hide #!1 models
> color #7 #b2b2ffff models
> color #7 #b2b2b2ff models
> color #7 #b2b2b293 models
> color #7 #b2b2b2ff models
> color #7 #b2b2b2de models
> color #7 #b2b2b2e0 models
> color #7 #b2b2b2e1 models
> volume #7 level 0.09416
> color #7 #b2b2b2ff models
> volume #7 level 0.095
> volume #7 level 0.09
> volume #4 level 0.19
> volume #6 level 0.07
> volume #6 level 0.0693
> volume #6 level 0.05518
> volume #7 color #b28fb2
> volume #7 color #698fb2
> volume #7 color #4d8fb2
> volume #1 color #b2b2b289
> open /Users/sunfh/Desktop/ARP/01_maps&models/3_ncBAF-NCP-
> Apo/J1462_J1431_zflip_3.11Amap.mrc
Opened J1462_J1431_zflip_3.11Amap.mrc as #8, grid size 432,432,432, pixel
0.93, shown at level 0.039, step 2, values float32
> hide #!7 models
> volume #8 level 0.07927
> volume #8 step 1
> volume #8 level 0.1035
> surface dust #1 size 9.3
> surface dust #8 size 9.3
> surface dust #1 size 9.3
> surface dust #8 size 9.3
> volume #1 level 0.03739
> volume #1 level 0.039
> volume #1 level 0.04
> volume #1 level 0.045
> volume #1 color #b2b2b242
> volume #1 color #b2b2b250
> volume #1 color #b2b2b2de
> volume #1 level 0.049
> volume #1 color #b2b2b25a
> volume #8 level 0.11
> volume #8 level 0.115
> volume #1 color #b2b2b291
> volume #1 color #b2b2b280
> volume #1 color #b2b2b267
> volume #1 color #b2b2b265
> volume #8 color #ffc2b2
> hide #!1 models
> show #!2 models
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/D
Alignment identifier is 2/D
> select #2/D:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/D:3-18
124 atoms, 123 bonds, 16 residues, 1 model selected
> show #!8 models
> color #8 #ffe9b2ff models
> color #8 #ffe9d6ff models
> color #8 #fff9d6ff models
> color #8 #fff9efff models
> color #8 #fff9dcff models
> color #8 #fff1dcff models
> volume zone #8 nearAtoms sel & #2 range 5.58
> hide #!8 models
> show #!8 models
> undo
> volume #8 level 0.1262
> volume #8 level 0.115
> volume #!8 style surface
> select add #8
124 atoms, 123 bonds, 16 residues, 3 models selected
> volume sel style surface
> hide #!2 models
> show #!2 models
> select subtract #8
124 atoms, 123 bonds, 16 residues, 1 model selected
> select add #2
23627 atoms, 24679 bonds, 4 pseudobonds, 2501 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #8
2 models selected
> volume sel style surface
> volume #8 style mesh
> volume #8 style surface
> color zone #8 near #2 distance 5.58
> hide #!2 models
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> show #!2 models
> volume #!8 style image
> hide #!2 models
> volume #8 style surface
> volume #8 style image
> volume #8 style surface
> volume #8 style image
> volume #8 level -0.007993,0 level 0.03897,0.8 level 0.7016,1
> volume #8 level -0.007993,0 level 0.1379,0.6 level 0.7016,1
> volume #8 style surface
> transparency #8.1 50
> volume #!8 style mesh
> volume #!8 style surface
> volume show
> volume hide
> show #!8 models
> hide #!8 models
> show #!4 models
> hide #!4 models
> show #!4 models
> vop gaussian #4 sdev 4.38
Opened cryosparc_P12_J2398_006_volume_map_Zflip.mrc gaussian as #9, grid size
192,192,192, pixel 1.46, shown at step 1, values float32
> volume #9 level 0.02704
> close #9
> volume #4 level 0.1851
> volume #4 level 0.207
> select add #8
3 models selected
> select add #8.2
3 models selected
> select add #8.2
3 models selected
> select add #8.2
3 models selected
> select add #8.2
3 models selected
> select add #8.2
3 models selected
> show #8.2 models
> select add #8
3 models selected
> select add #8
3 models selected
> select subtract #8.1
2 models selected
> select add #8.1
3 models selected
> select subtract #8.1
2 models selected
> hide #8.1 models
> show #8.1 models
> volume #8
> volume sel show
> show #8.2 models
> volume sel style surface
> volume sel style mesh
> volume sel style surface
> volume sel style image
> volume sel style surface
> transparency #8.1 0
> transparency #8.1 50
> volume sel style surface
> volume sel showOutlineBox true
> volume sel showOutlineBox false
> volume sel showOutlineBox true
> volume sel showOutlineBox false
> volume sel style surface
> close #8
> open /Users/sunfh/Desktop/ARP/01_maps&models/3_ncBAF-NCP-
> Apo/J1462_J1431_zflip_3.11Amap.mrc
Opened J1462_J1431_zflip_3.11Amap.mrc as #8, grid size 432,432,432, pixel
0.93, shown at level 0.039, step 2, values float32
> volume #8 level 0.1112
> surface dust #8 size 9.3
> volume #8 step 1
> volume #8 level 0.115
> color #8 #e5d499ff models
> color #8 #ffd499ff models
> color #8 #ffe699ff models
> color #8 #ffe6ceff models
> show #!2 models
> select #2/D:3-4
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/D:3-18
124 atoms, 123 bonds, 16 residues, 1 model selected
> color zone #8 near sel & #2 distance 5.58
> ui tool show "Color Zone"
> color zone #8 near #2 distance 5.97
> color zone #8 near #2 distance 2.99
> color single #8
> color zone #8 near sel distance 1.27
> color zone #8 near sel distance 1.18
> color zone #8 near sel distance 1.44
> color zone #8 near sel distance 1.5
> color zone #8 near sel distance 1.73
> color zone #8 near sel distance 1.76
> color zone #8 near sel distance 1.93
> color zone #8 near sel distance 1.97
> color zone #8 near sel distance 2
> color zone #8 near sel distance 1
> color zone #8 near sel distance 1.8
> color zone #8 near sel distance 1
> color zone #8 near sel distance 1.7
> color zone #8 near sel distance 1.67
> color zone #8 near sel distance 1.34
> color zone #8 near sel distance 2.16
> color zone #8 near sel distance 1.9
> color zone #8 near sel distance 2.59
> select add #2
23627 atoms, 24679 bonds, 4 pseudobonds, 2501 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!1 models
> show #!2 models
> select #2/D:3-4
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/D:3-18
124 atoms, 123 bonds, 16 residues, 1 model selected
> color sel blue
> color zone #8 near sel distance 2.59
> hide #!1 models
> color zone #8 near sel distance 2.5
> color zone #8 near sel distance 2.16
> select add #2
23627 atoms, 24679 bonds, 4 pseudobonds, 2501 residues, 2 models selected
> hide #!2 models
> select subtract #2
Nothing selected
> volume #1 color #b2b2b2b8
> volume #1 color #b2b2b263
> show #!2 models
> select #2/D:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/D:3-19
132 atoms, 131 bonds, 17 residues, 1 model selected
> view #2 clip false
> volume #1 color #b2b2b245
> volume #1 color #b2b2b250
> volume #1 level 0.05
> volume #1 level 0.055
> volume #1 level 0.052
> volume #1 color #b2b2b200
> select add #2
23627 atoms, 24679 bonds, 4 pseudobonds, 2501 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> volume #1 color #b2b2b20d
> volume #1 color #b2b2b214
> volume #1 color #b2b2b21a
> volume #1 color #b2b2b2
> volume #1 color #b2b2b228
> volume #1 level 0.055
> volume #1 level 0.05
> volume #1 color #b2b2b200
> volume #1 color #b2b2b21a
> volume #1 color #b2b2b226
> volume #1 color #b2b2b233
> volume #1 color #b2b2b24d
> volume #1 color #b2b2b233
> volume #1 color #b2b2b226
> volume #1 color #b2b2b21a
> volume #1 color #b2b2b2
> show #!6 models
> volume #1 color #b2b2b28f
> volume #1 color #b2b2b294
> volume #1 level 0.05
> volume #1 level 0.06679
> volume #1 level 0.07
> volume #1 color #b2b2b2
> volume #6 level 0.05009
> hide #!1 models
> hide #!6 models
> show #!2 models
> show #!3 models
Drag select of 197 atoms, 680 residues, 2 pseudobonds, 178 bonds
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!2 models
Drag select of 197 atoms, 845 residues, 2 pseudobonds, 178 bonds
> color (#!3 & sel) cornflower blue
> select clear
> show #!2 models
> hide #!3 models
Drag select of 795 residues, 2 pseudobonds
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Drag select of 109 residues
Drag select of 31 residues
Drag select of 767 residues, 2 pseudobonds
Drag select of 414 residues
Drag select of 768 residues, 2 pseudobonds
Drag select of 31 residues
Drag select of 170 residues
Drag select of 302 residues
> select clear
Drag select of 799 residues, 3 pseudobonds
> color (#!2 & sel) hot pink
> select clear
Drag select of 394 residues, 1 pseudobonds
> select #2/A:849
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:849
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:849
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
Drag select of 362 residues
> color sel hot pink
> select clear
> show #!3 models
> view #3 clip false
> select clear
Drag select of 197 atoms, 840 residues, 2 pseudobonds, 178 bonds
> color (#!3 & sel) dark gray
> select clear
Drag select of 24 residues
> color sel dark gray
> select clear
Drag select of 197 atoms, 845 residues, 2 pseudobonds, 178 bonds
> color (#!3 & sel) #d8ff32ff
> color (#!3 & sel) #d9ff32ff
> color (#!3 & sel) #f5ff50ff
> color (#!3 & sel) #fff643ff
> color (#!3 & sel) #ffdd44ff
> color (#!3 & sel) #fff55eff
> select clear
> save "/Users/sunfh/Desktop/ARP/nc-BAF-NCP maps.cxs"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406042103 (2024-06-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBookPro13,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 512.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.38f12
Software:
System Software Overview:
System Version: macOS 12.7 (21G816)
Kernel Version: Darwin 21.6.0
Time since boot: 5 days 2:16
Graphics/Displays:
Intel HD Graphics 530:
Chipset Model: Intel HD Graphics 530
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x191b
Revision ID: 0x0006
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 455:
Chipset Model: AMD Radeon Pro 455
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c7
ROM Revision: 113-C980AF-908
VBIOS Version: 113-C9801AP-028
EFI Driver Version: 01.A0.908
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
LS27A800U:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: HNMW400121
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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: 1.6.3
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
ChimeraX-AtomicLibrary: 14.0.5
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-clix: 0.1.6
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: 1.8rc202406042103
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: 1.5.16
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-NIHPresets: 1.1.19
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
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-QScore: 1.1
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-XMAS: 1.1.3
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
et-xmlfile: 1.1.0
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
openpyxl: 3.1.4
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.2
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: 3.0.46
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
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
seaborn: 0.13.2
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
traitlets: 5.14.2
typing-extensions: 4.12.1
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 , 14 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt 6.6 crash in displayConfigFinalizedProc. Probably connecting or disconnecting a display or waking from sleep.