![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Closed 2 months ago
#18735 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020c56e0c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio (total: 52)
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"codeSigningMonitor" : 2,
"incident" : "06FC450D-B2E4-4727-A30A-9B3825E43D5E",
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"procLaunch" : "2025-09-08 12:18:05.9141 +0900",
"procStartAbsTime" : 1267021135617,
"procExitAbsTime" : 1422976217508,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F0F130D3-F268-FD30-006B-5793B06DB6B6",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 6709,
"sleepWakeUUID" : "43371EE5-B312-445D-A41B-A778FA59C5F1",
"sip" : "enabled",
"vmRegionInfo" : "0x54693787b9c8 is not in any region. Bytes after previous region: 92329843603913 Bytes before following region: 12742236325432\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, 0x000054693787b9c8","rawCodes":[1,92810879941064],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000054693787b9c8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":13663},
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"name" : "libqtiff.dylib"
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{
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{
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"name" : "libqsvgicon.dylib"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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{
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"uuid" : "a55a4181-c446-3fa3-8fd6-27f845527eab",
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"name" : "_psutil_osx.abi3.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
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{
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
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{
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"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
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"uuid" : "c37482c0-7aab-3517-b3ef-3bd2294eab02",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
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{
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
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{
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"uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=9.9G written=5672K(0%) resident=5672K(0%) swapped_out=0K(0%) unallocated=9.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 832K 44 \nColorSync 624K 33 \nCoreAnimation 1424K 88 \nCoreGraphics 64K 4 \nCoreUI image data 5504K 53 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 8.8G 254 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 45 \nStack 203.5M 45 \nVM_ALLOCATE 575.5M 251 \nVM_ALLOCATE (reserved) 352.0M 4 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 34.0M 1082 \n__DATA_CONST 36.8M 1099 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.5M 150 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1069 \n__TEXT (graphics) 39.6M 50 \n__TPRO_CONST 128K 2 \ndyld private memory 2720K 24 \nmapped file 726.4M 98 \npage table in kernel 5672K 1 \nshared memory 3264K 29 \n=========== ======= ======= \nTOTAL 12.9G 6442 \nTOTAL, minus reserved VM space 12.5G 6442 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "32d1ed4969a2b0ff5987e5394586d293cbb52de8",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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},
{
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"factorPackIds" : {
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}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J85_004_volume_map_sharp.mrc"
Opened cryosparc_P17_J85_004_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 0.825, shown at level 0.0551, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J92_003_volume_map_sharp.mrc"
Opened cryosparc_P17_J92_003_volume_map_sharp.mrc as #2, grid size
448,448,448, pixel 0.825, shown at level 0.0581, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J93_004_volume_map_sharp.mrc"
Opened cryosparc_P17_J93_004_volume_map_sharp.mrc as #3, grid size
448,448,448, pixel 0.825, shown at level 0.0581, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J94_011_volume_map_sharp.mrc"
Opened cryosparc_P17_J94_011_volume_map_sharp.mrc as #4, grid size
448,448,448, pixel 0.825, shown at level 0.0515, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J86_009_volume_map_sharp.mrc"
Opened cryosparc_P17_J86_009_volume_map_sharp.mrc as #5, grid size
448,448,448, pixel 0.825, shown at level 0.0519, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J87_012_volume_map_sharp.mrc"
Opened cryosparc_P17_J87_012_volume_map_sharp.mrc as #6, grid size
448,448,448, pixel 0.825, shown at level 0.0528, step 2, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J88_009_volume_map_sharp.mrc"
Opened cryosparc_P17_J88_009_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.825, shown at level 0.0494, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J89_013_volume_map_sharp.mrc"
Opened cryosparc_P17_J89_013_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.825, shown at level 0.052, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J90_011_volume_map_sharp.mrc"
Opened cryosparc_P17_J90_011_volume_map_sharp.mrc as #9, grid size
448,448,448, pixel 0.825, shown at level 0.0544, step 2, values float32
> open "/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J91_004_volume_map_sharp.mrc"
Opened cryosparc_P17_J91_004_volume_map_sharp.mrc as #10, grid size
448,448,448, pixel 0.825, shown at level 0.0563, step 2, values float32
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!1 models
> volume #1 step 1
> surface dust #1 size 8.25
> hide #!1 models
> show #!2 models
> volume #2 step 1
> surface dust #2 size 8.25
> hide #!2 models
> volume #3 step 1
> show #!3 models
> surface dust #3 size 8.25
> hide #!3 models
> show #!4 models
> volume #4 step 1
> surface dust #4 size 8.25
> hide #!4 models
> show #!5 models
> volume #5 step 1
> surface dust #5 size 8.25
> hide #!5 models
> show #!6 models
> volume #6 step 1
> surface dust #6 size 8.25
> hide #!6 models
> show #!7 models
> volume #7 step 1
> surface dust #7 size 8.25
> hide #!7 models
> show #!8 models
> volume #8 step 1
> surface dust #8 size 8.25
> hide #!8 models
> show #!9 models
> volume #9 step 1
> surface dust #9 size 8.25
> hide #!9 models
> show #!10 models
> volume #10 step 1
> surface dust #10 size 8.25
> hide #!10 models
> show #!1 models
> volume #1 level 0.09254
> hide #!1 models
> show #!2 models
> volume #2 level 0.09078
> hide #!2 models
> show #!3 models
> volume #3 level 0.101
> hide #!3 models
> show #!4 models
> volume #4 level 0.09256
> hide #!4 models
> show #!5 models
> volume #5 level 0.07505
> volume #5 level 0.1008
> hide #!5 models
> show #!6 models
> volume #6 level 0.09509
> hide #!6 models
> show #!7 models
> volume #7 level 0.09016
> hide #!7 models
> show #!8 models
> volume #8 level 0.09118
> volume #8 level 0.09464
> hide #!8 models
> show #!9 models
> volume #9 level 0.09334
> volume #9 level 0.07
> volume #9 level 0.09983
> hide #!9 models
> show #!10 models
> volume #10 level 0.06798
> volume #10 level 0.09239
> volume #7 level 0.09
> hide #!10 models
> show #!7 models
> volume #1 level 0.09
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.09
> hide #!2 models
> show #!3 models
> volume #3 level 0.09
> hide #!3 models
> show #!4 models
> volume #4 level 0.09
> hide #!4 models
> show #!5 models
> volume #5 level 0.09
> hide #!5 models
> show #!6 models
> volume #6 level 0.09
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> volume #8 level 0.09
> hide #!8 models
> show #!9 models
> volume #9 level 0.09
> hide #!9 models
> show #!10 models
> volume #10 level 0.09
> hide #!10 models
> show #!1 models
> set bgColor white
> set bgColor #ffffff00
> save /Users/uozumilab2/Desktop/image1.png supersample 3
> hide #!1 models
> show #!2 models
> save /Users/uozumilab2/Desktop/image2.png supersample 3
> hide #!2 models
> show #!3 models
> save /Users/uozumilab2/Desktop/image3.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/uozumilab2/Desktop/image4.png supersample 3
> hide #!4 models
> show #!5 models
> save /Users/uozumilab2/Desktop/image5.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/uozumilab2/Desktop/image6.png supersample 3
> hide #!6 models
> show #!7 models
> save /Users/uozumilab2/Desktop/image7.png supersample 3
> hide #!7 models
> show #!8 models
> save /Users/uozumilab2/Desktop/image8.png supersample 3
> hide #!8 models
> show #!9 models
> save /Users/uozumilab2/Desktop/image9.png supersample 3
> hide #!9 models
> show #!10 models
> save /Users/uozumilab2/Desktop/image10.png supersample 3
> volume #10 level 0.01
> volume #10 level 0.04
> volume #10 level 0.05
> volume #9 level 0.05
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!1 models
> volume #1 level 0.05
> volume #2 level 0.05
> volume #3 level 0.05
> volume #4 level 0.05
> volume #5 level 0.05
> volume #6 level 0.05
> volume #7 level 0.05
> volume #8 level 0.05
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> turn y 90
> view orient
> ui tool show "Side View"
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> turn y 90
> turn x 90
> hide #!2 models
> turn y 90
> turn y 10
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!1 models
> save /Users/uozumilab2/Desktop/image1.png supersample 3
> hide #!1 models
> show #!2 models
> show #!1 models
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.21839,0.97517,-0.036731,-28.644,-0.97586,0.21818,-0.009868,326.73,-0.0016092,0.037999,0.99928,-6.5845
> fitmap #2 inMap #1
Fit map cryosparc_P17_J92_003_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 1159088 points
correlation = 0.9089, correlation about mean = 0.6679, overlap = 5976
steps = 68, shift = 0.931, angle = 3.22 degrees
Position of cryosparc_P17_J92_003_volume_map_sharp.mrc (#2) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.25846076 0.96602175 0.00007346 -41.49098775
-0.96602176 0.25846076 -0.00003058 315.55988283
-0.00004853 -0.00006306 1.00000000 -0.30844972
Axis -0.00001681 0.00006314 -1.00000000
Axis point 184.79838080 184.80560309 0.00000000
Rotation angle (degrees) 75.02125128
Shift along axis 0.32907104
> turn x 90
> select subtract #2
Nothing selected
> hide #!1 models
> save /Users/uozumilab2/Desktop/image2.png supersample 3
> hide #!2 models
> show #!3 models
> show #!1 models
> select ~sel & ##selected
Nothing selected
> select down
Nothing selected
> turn x -90
> select add #3
2 models selected
> view matrix models
> #3,0.77789,0.62818,-0.016757,-71.388,-0.62837,0.77783,-0.011417,159.67,0.0058623,0.019411,0.99979,-4.6258
> fitmap #3 inMap #1
Fit map cryosparc_P17_J93_004_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 1133741 points
correlation = 0.9465, correlation about mean = 0.7769, overlap = 6901
steps = 100, shift = 0.919, angle = 6.42 degrees
Position of cryosparc_P17_J93_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84231178 0.53899059 0.00008646 -70.47272760
-0.53899059 0.84231179 -0.00002221 128.74734890
-0.00008480 -0.00002790 1.00000000 -0.38680135
Axis -0.00000528 0.00015887 -0.99999999
Axis point 184.79775712 184.81427456 0.00000000
Rotation angle (degrees) 32.61495056
Shift along axis 0.40762767
> select subtract #3
Nothing selected
> turn x 90
> hide #!1 models
> volume #3 level 0.04322
> volume #3 level 0.05
> save /Users/uozumilab2/Desktop/image3.png supersample 3
> hide #!3 models
> show #!4 models
> show #!1 models
> turn x -90
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> turn x 90
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #1 inMap #4
Fit map cryosparc_P17_J85_004_volume_map_sharp.mrc in map
cryosparc_P17_J94_011_volume_map_sharp.mrc using 1042243 points
correlation = 0.8973, correlation about mean = 0.5035, overlap = 5669
steps = 56, shift = 0.364, angle = 0.967 degrees
Position of cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99985771 0.01686916 -0.00000694 -3.07909934
-0.01686916 0.99985771 -0.00000001 3.14503024
0.00000694 0.00000013 1.00000000 0.36302770
Axis 0.00000427 -0.00041143 -0.99999992
Axis point 184.87493376 184.08762582 0.00000000
Rotation angle (degrees) 0.96657787
Shift along axis -0.36433478
> hide #!1 models
> save /Users/uozumilab2/Desktop/image4.png supersample 3
> hide #!4 models
> show #!5 models
> show #!1 models
> turn x -90
> select add #5
2 models selected
> view matrix models
> #5,0.61829,0.7856,-0.023507,-69.616,-0.78593,0.61819,-0.012409,218.45,0.004783,0.026147,0.99965,-5.6404
> fitmap #5 inMap #1
Fit map cryosparc_P17_J86_009_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 956200 points
correlation = 0.8835, correlation about mean = 0.4981, overlap = 5570
steps = 120, shift = 0.833, angle = 11.5 degrees
Position of cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.77271076 0.63475829 -0.00001580 -75.30664248
-0.63475829 0.77271076 -0.00000450 159.31066717
0.00000935 0.00001350 1.00000000 -0.41824436
Axis 0.00001418 -0.00001981 -1.00000000
Axis point 184.80280856 184.81103885 0.00000000
Rotation angle (degrees) 39.40205947
Shift along axis 0.41402097
> select subtract #5
Nothing selected
> turn x 90
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/uozumilab2/Desktop/image5.png supersample 3
> hide #!5 models
> show #!6 models
> show #!1 models
> turn x -90
> select add #6
2 models selected
> view matrix models
> #6,0.62926,0.77685,-0.02308,-70.182,-0.77718,0.62916,-0.012392,214.77,0.0048945,0.025735,0.99966,-5.588
> fitmap #6 inMap #1
Fit map cryosparc_P17_J87_012_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 992914 points
correlation = 0.8894, correlation about mean = 0.5052, overlap = 5645
steps = 60, shift = 0.8, angle = 1.93 degrees
Position of cryosparc_P17_J87_012_volume_map_sharp.mrc (#6) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.65840925 0.75266012 0.00004024 -75.96680112
-0.75266012 0.65840925 -0.00000944 202.21774655
-0.00003360 -0.00002407 1.00000000 -0.15421395
Axis -0.00000972 0.00004906 -1.00000000
Axis point 184.79960514 184.80138827 0.00000000
Rotation angle (degrees) 48.82133441
Shift along axis 0.16487213
> select subtract #6
Nothing selected
> turn x 90
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/uozumilab2/Desktop/image6.png supersample 3
> hide #!6 models
> show #!7 models
> show #!1 models
> turn x -90
> hide #!1 models
> save /Users/uozumilab2/Desktop/image7.png supersample 3
> hide #!7 models
> show #!8 models
> show #!1 models
> turn x -90
> undo
> turn x -90
> select add #8
2 models selected
> view matrix models
> #8,-0.91104,-0.41042,-0.039498,437.56,0.40873,-0.91157,0.044439,268.1,-0.054244,0.024342,0.99823,5.909
> select subtract #8
Nothing selected
> fitmap #1 inMap #8
Fit map cryosparc_P17_J85_004_volume_map_sharp.mrc in map
cryosparc_P17_J89_013_volume_map_sharp.mrc using 1042243 points
correlation = 0.9097, correlation about mean = 0.5305, overlap = 5841
steps = 104, shift = 1.93, angle = 7.37 degrees
Position of cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.95780920 0.28740483 0.00005167 308.67743001
-0.28740483 -0.95780920 -0.00001131 414.91853351
0.00004624 -0.00002568 0.99999999 0.38613934
Axis -0.00002501 0.00000945 -1.00000000
Axis point 184.79356578 184.80246870 0.00000000
Rotation angle (degrees) 163.29734922
Shift along axis -0.38993909
> turn x -90
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/uozumilab2/Desktop/image8.png supersample 3
> hide #!8 models
> show #!9 models
> show #!1 models
> turn x -90
> fitmap #1 inMap #9
Fit map cryosparc_P17_J85_004_volume_map_sharp.mrc in map
cryosparc_P17_J90_011_volume_map_sharp.mrc using 1042243 points
correlation = 0.9001, correlation about mean = 0.506, overlap = 6055
steps = 104, shift = 1.95, angle = 7.16 degrees
Position of cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.99978055 0.02094856 0.00003510 -3.83295378
-0.02094856 0.99978055 -0.00001338 3.91247392
-0.00003538 0.00001265 1.00000000 0.15375152
Axis 0.00062132 0.00168223 -0.99999839
Axis point 184.84087475 184.90167151 0.00000000
Rotation angle (degrees) 1.20035369
Shift along axis -0.14955106
> hide #!1 models
> turn x -90
> save /Users/uozumilab2/Desktop/image9.png supersample 3
> hide #!9 models
> show #!10 models
> show #!1 models
> turn x -90
> select add #10
2 models selected
> view matrix models
> #10,-0.37088,0.92732,-0.050327,92.879,-0.92853,-0.37126,0.0019041,424.59,-0.016918,0.047436,0.99873,-5.3645
> fitmap #10 inMap #1
Fit map cryosparc_P17_J91_004_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 1090866 points
correlation = 0.9531, correlation about mean = 0.7872, overlap = 6824
steps = 140, shift = 1.58, angle = 14.3 degrees
Position of cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.11549341 0.99330825 0.00003435 22.58241347
-0.99330825 -0.11549341 -0.00002197 389.70596942
-0.00001785 -0.00003666 1.00000000 -0.35214737
Axis -0.00000740 0.00002628 -1.00000000
Axis point 184.80103765 184.79855038 0.00000000
Rotation angle (degrees) 96.63208510
Shift along axis 0.36222148
> select subtract #10
Nothing selected
> turn x 90
> hide #!1 models
> save /Users/uozumilab2/Desktop/image10.png supersample 3
> hide #!10 models
> show #!1 models
> turn x -90
> save /Users/uozumilab2/Desktop/image11.png supersample 3
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/uozumilab2/Desktop/image12.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/uozumilab2/Desktop/image13.png supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!5 models
> save /Users/uozumilab2/Desktop/image14.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/uozumilab2/Desktop/image15.png supersample 3
> hide #!6 models
> show #!7 models
> save /Users/uozumilab2/Desktop/image16.png supersample 3
> hide #!7 models
> show #!8 models
> save /Users/uozumilab2/Desktop/image17.png supersample 3
> hide #!8 models
> show #!9 models
> save /Users/uozumilab2/Desktop/image18.png supersample 3
> hide #!9 models
> show #!10 models
> save /Users/uozumilab2/Desktop/image19.png supersample 3
> hide #!10 models
> show #!4 models
> view
> ui tool show "Side View"
> hide #!4 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> save /Users/uozumilab2/Desktop/image20.png supersample 3
> hide #!1 models
> show #!2 models
> save /Users/uozumilab2/Desktop/image21.png supersample 3
> hide #!2 models
> show #!3 models
> save /Users/uozumilab2/Desktop/image22.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/uozumilab2/Desktop/image23.png supersample 3
> hide #!4 models
> show #!5 models
> save /Users/uozumilab2/Desktop/image24.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/uozumilab2/Desktop/image25.png supersample 3
> hide #!6 models
> show #!7 models
> save /Users/uozumilab2/Desktop/image26.png supersample 3
> hide #!7 models
> show #!8 models
> save /Users/uozumilab2/Desktop/image27.png supersample 3
> hide #!8 models
> show #!9 models
> save /Users/uozumilab2/Desktop/image28.png supersample 3
> hide #!9 models
> show #!10 models
> save /Users/uozumilab2/Desktop/image29.png supersample 3
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!10 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> open /Users/uozumilab2/Downloads/9L9U-assembly1.cif.gz
File reader requires uncompressed file;
'/Users/uozumilab2/Downloads/9L9U-assembly1.cif.gz' is compressed
> open /Users/uozumilab2/Downloads/9L9U.cif
9L9U.cif title:
Arabidopsis GORK WT1 [more info...]
Chain information for 9L9U.cif #11
---
Chain | Description | UniProt
A B C D | Potassium channel GORK | GORK_ARATH 2-820
> volume #4 level 0.08996
> select add #11
21836 atoms, 22345 bonds, 2692 residues, 1 model selected
> view matrix models
> #11,0.9973,-0.0030636,-0.073386,14.477,0.0012426,0.99969,-0.024847,4.4479,0.07344,0.024689,0.99699,-14.873
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.9973,-0.0030636,-0.073386,44.268,0.0012426,0.99969,-0.024847,25.649,0.07344,0.024689,0.99699,-9.765
> view matrix models
> #11,0.9973,-0.0030636,-0.073386,37.293,0.0012426,0.99969,-0.024847,23.896,0.07344,0.024689,0.99699,4.9111
> view matrix models
> #11,0.9973,-0.0030636,-0.073386,36.524,0.0012426,0.99969,-0.024847,23.46,0.07344,0.024689,0.99699,6.9891
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.5586,-0.82549,-0.080874,236.84,0.82757,0.56123,-0.012445,-39.13,0.055662,-0.059977,0.99665,23.236
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.5586,-0.82549,-0.080874,238.29,0.82757,0.56123,-0.012445,-31.828,0.055662,-0.059977,0.99665,23.553
> view matrix models
> #11,0.5586,-0.82549,-0.080874,237.69,0.82757,0.56123,-0.012445,-31.904,0.055662,-0.059977,0.99665,27.775
> fitmap #11 inMap #4
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms
average map value = 0.08035, steps = 2000
shifted from previous position = 3.6
rotated from previous position = 6.79 degrees
atoms outside contour = 14758, contour level = 0.089962
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.48947063 -0.87201611 0.00252961 244.54001690
0.87201612 0.48945810 -0.00431944 -29.24784000
0.00252848 0.00432010 0.99998747 26.67111281
Axis 0.00495371 0.00000065 0.99998773
Axis point 147.18253319 194.10293925 0.00000000
Rotation angle (degrees) 60.69502962
Shift along axis 27.88214688
> transparency #4.1 50
> select subtract #11
Nothing selected
> volume #4 level 0.08108
> volume #4 level 0.06998
> hide #!4 models
> hide #11 models
> open /Users/uozumilab2/Downloads/9LA0.cif
9LA0.cif title:
Arabidopsis GORK WT5 [more info...]
Chain information for 9LA0.cif #12
---
Chain | Description | UniProt
A B C D | Potassium channel GORK | GORK_ARATH 2-820
> show #!4 models
> volume #4 level 0.09551
> select add #12
21944 atoms, 22460 bonds, 2704 residues, 1 model selected
> view matrix models #12,1,0,0,30.488,0,1,0,33.189,0,0,1,-1.3523
> view matrix models #12,1,0,0,30.977,0,1,0,29.448,0,0,1,27.556
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.9178,-0.37059,-0.14251,128.25,0.38888,0.91145,0.13428,-42.514,0.080127,-0.17866,0.98064,46.543
> view matrix models
> #12,0.55709,-0.80017,-0.2222,267.16,0.83024,0.54269,0.12724,-52.832,0.018772,-0.25536,0.96666,70.819
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.55709,-0.80017,-0.2222,256.99,0.83024,0.54269,0.12724,-51.957,0.018772,-0.25536,0.96666,69.042
> view matrix models
> #12,0.55709,-0.80017,-0.2222,255.68,0.83024,0.54269,0.12724,-50.259,0.018772,-0.25536,0.96666,69.666
> view matrix models
> #12,0.55709,-0.80017,-0.2222,255.77,0.83024,0.54269,0.12724,-50.297,0.018772,-0.25536,0.96666,68.727
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.55555,-0.82478,-0.10533,238.46,0.82714,0.56113,-0.031238,-23.662,0.084867,-0.069767,0.99395,24.162
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.55555,-0.82478,-0.10533,238.27,0.82714,0.56113,-0.031238,-31.329,0.084867,-0.069767,0.99395,23.894
> view matrix models
> #12,0.55555,-0.82478,-0.10533,238.33,0.82714,0.56113,-0.031238,-31.327,0.084867,-0.069767,0.99395,23.663
> fitmap #12 inMap #4
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21944 atoms
average map value = 0.07179, steps = 2000
shifted from previous position = 8.72
rotated from previous position = 7.7 degrees
atoms outside contour = 16036, contour level = 0.095512
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.50309993 -0.86420599 0.00620231 240.71249764
0.86421754 0.50311646 0.00136631 -30.79714710
-0.00430126 0.00467275 0.99997983 27.96715983
Axis 0.00191294 0.00607684 0.99997971
Axis point 147.26102230 193.80155398 0.00000000
Rotation angle (degrees) 59.79481813
Shift along axis 28.23991177
> select subtract #12
Nothing selected
> select add #12
21944 atoms, 22460 bonds, 2704 residues, 1 model selected
> view matrix models
> #12,0.5031,-0.86421,0.0062023,240.42,0.86422,0.50312,0.0013663,-30.815,-0.0043013,0.0046728,0.99998,26.914
> view matrix models
> #12,0.5031,-0.86421,0.0062023,239.73,0.86422,0.50312,0.0013663,-31.281,-0.0043013,0.0046728,0.99998,26.533
> fitmap #12 inMap #4
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21944 atoms
average map value = 0.07158, steps = 2000
shifted from previous position = 1.71
rotated from previous position = 0.274 degrees
atoms outside contour = 16050, contour level = 0.095512
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.50322986 -0.86414973 0.00222580 241.12022280
0.86415260 0.50322819 -0.00129768 -30.21436053
0.00000131 0.00257646 0.99999668 27.61855575
Axis 0.00224158 0.00128709 0.99999666
Axis point 146.84021313 194.53961587 0.00000000
Rotation angle (degrees) 59.78624859
Shift along axis 28.12006572
> select subtract #12
Nothing selected
> hide #12 models
> show #11 models
> view
> fitmap #11 inMap #4
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms
average map value = 0.0804, steps = 2000
shifted from previous position = 0.411
rotated from previous position = 0.332 degrees
atoms outside contour = 15399, contour level = 0.095512
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.48969651 -0.87189244 0.00095120 244.94607476
0.87189158 0.48969738 0.00124112 -29.98918017
-0.00154793 0.00022157 0.99999878 28.21878535
Axis -0.00058468 0.00143316 0.99999880
Axis point 148.13504908 194.25404443 0.00000000
Rotation angle (degrees) 60.67937541
Shift along axis 28.03255797
> volume #4 level 0.08552
> fitmap #11 inMap #4
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms
average map value = 0.08019, steps = 2000
shifted from previous position = 0.354
rotated from previous position = 0.0647 degrees
atoms outside contour = 14056, contour level = 0.085521
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.48975829 -0.87185824 -0.00017355 244.82122570
0.87185763 0.48975768 0.00130095 -30.15912233
-0.00104924 -0.00078846 0.99999914 28.37790838
Axis -0.00119825 0.00050220 0.99999916
Axis point 148.20634470 194.10701492 0.00000000
Rotation angle (degrees) 60.67535250
Shift along axis 28.06938147
> hide #11 models
> show #11 models
> hide #11 models
> show #!1 models
> hide #!4 models
> show #11 models
> transparency #1.1 50
> volume #1 level 0.09901
> hide #11 models
> show #12 models
> hide #12 models
> show #11 models
> hide #!1 models
> show #!2 models
> transparency #2.1 50
> volume #2 level 0.05601
> volume #2 level 0.07068
> hide #!2 models
> show #!3 models
> transparency #3.1 50
> volume #3 level 0.09518
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> transparency #5.1 50
> volume #5 level 0.08609
> fitmap #11 inMap #5
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21836 atoms
average map value = 0.08371, steps = 2000
shifted from previous position = 0.471
rotated from previous position = 0.396 degrees
atoms outside contour = 13749, contour level = 0.086085
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.18854667 -0.98205718 0.00372226 368.89610343
0.98205539 -0.18852754 0.00495720 58.90982444
-0.00416650 0.00459012 0.99998078 28.16331907
Axis -0.00018689 0.00401642 0.99999192
Axis point 160.15969433 181.80624398 0.00000000
Rotation angle (degrees) 100.86798412
Shift along axis 28.33075581
> volume #5 level 0.08093
> hide #!5 models
> show #!6 models
> transparency #6.1 50
> volume #6 level 0.07232
> volume #6 level 0.06645
> volume #6 level 0.07584
> hide #!6 models
> show #!7 models
> transparency #7.1 50
> volume #7 level 0.0848
> hide #!7 models
> show #!8 models
> transparency #8.1 50
> volume #8 level 0.08803
> fitmap #11 inMap #8
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J89_013_volume_map_sharp.mrc
(#8) using 21836 atoms
average map value = 0.08195, steps = 2000
shifted from previous position = 0.754
rotated from previous position = 7.02 degrees
atoms outside contour = 14343, contour level = 0.088031
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.19683143 0.98043723 -0.00047197 61.33981057
-0.98043690 -0.19683086 0.00104141 370.41851312
0.00092813 0.00066772 0.99999934 27.55524391
Axis -0.00019057 -0.00071402 -0.99999973
Axis point 182.38152037 160.07697775 0.00000000
Rotation angle (degrees) 101.35173302
Shift along axis -27.83141248
> volume #8 level 0.08342
> hide #!8 models
> show #!9 models
> transparency #9.1 50
> volume #9 level 0.09021
> volume #9 level 0.08632
> hide #!9 models
> show #!10 models
> transparency #10.1 50
> volume #10 level 0.08608
> fitmap #11 inMap #10
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms
average map value = 0.0748, steps = 100
shifted from previous position = 0.811
rotated from previous position = 7.46 degrees
atoms outside contour = 14299, contour level = 0.086082
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93258114 -0.36095219 -0.00243413 389.10299366
0.36093541 -0.93257473 0.00547641 274.01040811
-0.00424673 0.00422864 0.99998204 27.97315722
Axis -0.00172848 0.00251091 0.99999535
Axis point 168.99392239 173.31077389 0.00000000
Rotation angle (degrees) 158.84172756
Shift along axis 27.98848463
> view orient
> fitmap #11 inMap #10
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms
average map value = 0.0748, steps = 28
shifted from previous position = 0.015
rotated from previous position = 0.00553 degrees
atoms outside contour = 14299, contour level = 0.086082
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93259818 -0.36090821 -0.00242805 389.09908210
0.36089182 -0.93259209 0.00539237 274.02005349
-0.00421053 0.00415266 0.99998251 27.98156603
Axis -0.00171753 0.00246948 0.99999548
Axis point 168.99414628 173.31103546 0.00000000
Rotation angle (degrees) 158.84442047
Shift along axis 27.98983917
> hide #!10 models
> show #!5 models
> undo
> show #!5 models
> view orient
> ui tool show "Side View"
> transparency #5.1 0
> volume #!5 style mesh
> volume #!5 style surface
> volume #!5 style image
> volume #!5 style surface
> volume #!5 style mesh
> volume #!5 style surface
> volume #!5 style mesh
> volume #!5 style image
> volume #!5 style mesh
> volume #!5 style surface
> volume #!5 showOutlineBox true
> transparency #5.1 50
> volume #!5 showOutlineBox false
> volume #!5 style mesh
> volume #!5 style surface
> hide #11 models
> show #12 models
> fitmap #12 inMap #5
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21944 atoms
average map value = 0.07408, steps = 2000
shifted from previous position = 0.529
rotated from previous position = 0.483 degrees
atoms outside contour = 14188, contour level = 0.08093
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.17148280 -0.98516145 0.00711053 366.04943852
0.98517789 -0.17144550 0.00556400 55.71901988
-0.00426237 0.00795927 0.99995924 27.61974939
Axis 0.00121564 0.00577195 0.99998260
Axis point 159.64732348 181.68680593 0.00000000
Rotation angle (degrees) 99.87414412
Shift along axis 28.38586101
> hide #12 models
> volume #5 level 0.08
> volume #5 change image level -0.005746,0 level 0.05178,0.8 level 0.4066,1
> show #11 models
> volume #5 level 0.09
> volume #5 level 0.05
> volume #5 level 0.09
> undo
> show #11 models
> view orient
> fitmap #11 inMap #5
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21836 atoms
average map value = 0.08378, steps = 2000
shifted from previous position = 0.121
rotated from previous position = 0.521 degrees
atoms outside contour = 14347, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.18871694 -0.98203093 0.00107831 369.28206341
0.98202319 -0.18871070 0.00432742 59.11782565
-0.00404617 0.00187558 0.99999005 28.19901947
Axis -0.00124835 0.00260912 0.99999582
Axis point 160.26921285 182.07385197 0.00000000
Rotation angle (degrees) 100.87802359
Shift along axis 27.89215469
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A #11/B #11/C #11/D #12/A #12/B #12/C #12/D
Alignment identifier is 1
> select #11/A-D:511-512 #12/A-D:511-512
152 atoms, 144 bonds, 16 residues, 2 models selected
> select #11/A-D:511-519 #12/A-D:511-519
608 atoms, 600 bonds, 72 residues, 2 models selected
Potassium Channel GORK [ID: 1] region 8 chains [519-527] RMSD: 6.546
> color (#11 & sel) red
> select add #11
22140 atoms, 22645 bonds, 2728 residues, 2 models selected
> select add #12
43780 atoms, 44805 bonds, 5396 residues, 2 models selected
> select subtract #11
21944 atoms, 22460 bonds, 2704 residues, 1 model selected
> select subtract #12
Nothing selected
> volume #1 level 0.09
> volume #2 level 0.09
> volume #3 level 0.09
> volume #4 level 0.09
> volume #6 level 0.09
> volume #7 level 0.09
> volume #8 level 0.09
> volume #9 level 0.09
> volume #10 level 0.09
> save /Users/uozumilab2/Desktop/image1.png supersample 3
> hide #!5 models
> show #!1 models
> save /Users/uozumilab2/Desktop/image1.png supersample 3
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.05
> volume #1 level 0.05
> hide #!2 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.05
> volume #4 level 0.05
> volume #5 level 0.05
> volume #6 level 0.05
> volume #7 level 0.05
> volume #8 level 0.05
> volume #9 level 0.05
> volume #10 level 0.05
> show #!1 models
> volume #1 level 0.06
> volume #1 level 0.07
> volume #1 level 0.08
> volume #1 level 0.09
> save /Users/uozumilab2/Desktop/image1.png supersample 3
> hide #!1 models
> show #!2 models
> volume #2 level 0.06
> volume #2 level 0.07
> volume #2 level 0.08
> volume #2 level 0.05
> volume #2 level 0.06
> volume #2 level 0.09
> volume #2 level 0.05
> save /Users/uozumilab2/Desktop/image2.png supersample 3
> hide #!2 models
> show #!3 models
> volume #3 level 0.09
> volume #4 level 0.09
> volume #5 level 0.09
> volume #6 level 0.09
> volume #7 level 0.09
> volume #8 level 0.09
> volume #9 level 0.09
> volume #10 level 0.09
> save /Users/uozumilab2/Desktop/image2.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/uozumilab2/Desktop/image3.png supersample 3
> hide #!4 models
> show #!5 models
> save /Users/uozumilab2/Desktop/image4.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/uozumilab2/Desktop/image5.png supersample 3
> hide #!6 models
> show #!7 models
> save /Users/uozumilab2/Desktop/image6.png supersample 3
> hide #!7 models
> show #!8 models
> save /Users/uozumilab2/Desktop/image7.png supersample 3
> hide #!8 models
> show #!9 models
> save /Users/uozumilab2/Desktop/image8.png supersample 3
> fitmap #11 inMap #9
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J90_011_volume_map_sharp.mrc
(#9) using 21836 atoms
average map value = 0.08549, steps = 2000
shifted from previous position = 0.478
rotated from previous position = 0.453 degrees
atoms outside contour = 14092, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.48761455 -0.87305662 -0.00204759 245.65931372
0.87305901 0.48761301 0.00122888 -30.01779299
-0.00007445 -0.00238689 0.99999715 28.30342300
Axis -0.00207074 -0.00113002 0.99999722
Axis point 148.40598626 194.34692887 0.00000000
Rotation angle (degrees) 60.81623085
Shift along axis 27.82856780
> hide #!9 models
> show #!10 models
> fitmap #11 inMap #10
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms
average map value = 0.0748, steps = 48
shifted from previous position = 0.4
rotated from previous position = 0.489 degrees
atoms outside contour = 14961, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93259707 -0.36091101 -0.00243967 389.09971033
0.36089450 -0.93259097 0.00540756 274.02777352
-0.00422686 0.00416261 0.99998240 27.98060976
Axis -0.00172476 0.00247599 0.99999545
Axis point 168.99364652 173.31518114 0.00000000
Rotation angle (degrees) 158.84425132
Shift along axis 27.98786816
> hide #!10 models
> show #!1 models
> fitmap #11 inMap #1
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J85_004_volume_map_sharp.mrc
(#1) using 21836 atoms
average map value = 0.07957, steps = 84
shifted from previous position = 0.164
rotated from previous position = 0.154 degrees
atoms outside contour = 13862, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.46838416 -0.88351193 0.00479113 249.43621126
0.88351855 0.46839448 0.00125602 -28.52533883
-0.00335384 0.00364475 0.99998773 27.72112460
Axis 0.00135182 0.00460936 0.99998846
Axis point 148.51058363 192.92085980 0.00000000
Rotation angle (degrees) 62.07060324
Shift along axis 27.92651425
> save /Users/uozumilab2/Desktop/image1.png supersample 3
> hide #!1 models
> show #!2 models
> fitmap #11 inMap #2
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J92_003_volume_map_sharp.mrc
(#2) using 21836 atoms
average map value = 0.06074, steps = 120
shifted from previous position = 0.747
rotated from previous position = 1.24 degrees
atoms outside contour = 8755, contour level = 0.05
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J92_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.73280010 -0.68044374 0.00057594 407.50866351
0.68044226 -0.73279607 0.00287364 192.49988169
-0.00153331 0.00249770 0.99999570 27.35154803
Axis -0.00027625 0.00154990 0.99999876
Axis point 165.97058019 176.24151103 0.00000000
Rotation angle (degrees) 137.12166393
Shift along axis 27.53729629
> save /Users/uozumilab2/Desktop/image2.png supersample 3
> hide #!2 models
> show #!3 models
> fitmap #11 inMap #3
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J93_004_volume_map_sharp.mrc
(#3) using 21836 atoms
average map value = 0.07199, steps = 44
shifted from previous position = 0.314
rotated from previous position = 0.142 degrees
atoms outside contour = 15368, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J93_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.08403690 -0.99646224 0.00089893 354.88117594
0.99646230 -0.08403610 0.00089980 40.72620654
-0.00082107 0.00097137 0.99999919 27.86137784
Axis 0.00003591 0.00086306 0.99999963
Axis point 158.73308781 183.45667504 0.00000000
Rotation angle (degrees) 94.82064536
Shift along axis 27.90926032
> save /Users/uozumilab2/Desktop/image2.png supersample 3
> hide #!3 models
> show #!4 models
> fitmap #11 inMap #4
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms
average map value = 0.08023, steps = 2000
shifted from previous position = 0.447
rotated from previous position = 1.54 degrees
atoms outside contour = 14788, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.48944822 -0.87201097 0.00610822 244.29229162
0.87202360 0.48946270 0.00105376 -30.11457588
-0.00390864 0.00481075 0.99998079 27.57199436
Axis 0.00215415 0.00574339 0.99998119
Axis point 147.97196306 193.44342631 0.00000000
Rotation angle (degrees) 60.69583421
Shift along axis 27.92475879
> save /Users/uozumilab2/Desktop/image3.png supersample 3
> hide #!4 models
> show #!5 models
> fitmap #11 inMap #5
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21836 atoms
average map value = 0.08382, steps = 2000
shifted from previous position = 0.571
rotated from previous position = 0.427 degrees
atoms outside contour = 14308, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.18857013 -0.98205797 -0.00185779 369.55313334
0.98205777 -0.18857320 0.00163930 59.51404927
-0.00196021 -0.00151533 0.99999693 28.73218084
Axis -0.00160613 0.00005215 0.99999871
Axis point 160.21346018 182.44686607 0.00000000
Rotation angle (degrees) 100.86952953
Shift along axis 28.14169734
> save /Users/uozumilab2/Desktop/image4.png supersample 3
> hide #!5 models
> show #!6 models
> fitmap #11 inMap #6
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J87_012_volume_map_sharp.mrc
(#6) using 21836 atoms
average map value = 0.08248, steps = 2000
shifted from previous position = 0.31
rotated from previous position = 0.651 degrees
atoms outside contour = 14745, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J87_012_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.35694611 -0.93412417 -0.00122969 388.34936101
0.93411415 -0.35694801 0.00434374 93.02447560
-0.00449653 0.00040181 0.99998981 28.28765327
Axis -0.00210996 0.00174861 0.99999625
Axis point 162.20211864 180.17746706 0.00000000
Rotation angle (degrees) 110.91313503
Shift along axis 27.63080797
> save /Users/uozumilab2/Desktop/image5.png supersample 3
> hide #!6 models
> show #!7 models
> fitmap #11 inMap #7
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J88_009_volume_map_sharp.mrc
(#7) using 21836 atoms
average map value = 0.08656, steps = 2000
shifted from previous position = 0.577
rotated from previous position = 3.55 degrees
atoms outside contour = 13674, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J88_009_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.53604381 -0.84418288 0.00350765 232.71001494
0.84418877 0.53604584 -0.00041358 -32.86953052
-0.00153112 0.00318282 0.99999376 28.07683083
Axis 0.00213008 0.00298438 0.99999328
Axis point 146.30635837 195.18237933 0.00000000
Rotation angle (degrees) 57.58541494
Shift along axis 28.47423851
> save /Users/uozumilab2/Desktop/image6.png supersample 3
> hide #!7 models
> show #!8 models
> save /Users/uozumilab2/Desktop/image7.png supersample 3
> fitmap #11 inMap #8
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J89_013_volume_map_sharp.mrc
(#8) using 21836 atoms
average map value = 0.08199, steps = 2000
shifted from previous position = 0.731
rotated from previous position = 4.79 degrees
atoms outside contour = 14668, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.19689966 0.98042102 -0.00226852 61.79924268
-0.98040026 -0.19691042 -0.00645019 371.30478268
-0.00677059 0.00095401 0.99997662 28.73732717
Axis 0.00377603 0.00229599 -0.99999023
Axis point 183.05322918 160.33182754 0.00000000
Rotation angle (degrees) 101.35671540
Shift along axis -27.65117702
> save /Users/uozumilab2/Desktop/image7.png supersample 3
> hide #!8 models
> show #!9 models
> fitmap #11 inMap #9
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J90_011_volume_map_sharp.mrc
(#9) using 21836 atoms
average map value = 0.08547, steps = 2000
shifted from previous position = 0.783
rotated from previous position = 7.25 degrees
atoms outside contour = 14170, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.48744965 -0.87314518 0.00321498 244.91335655
0.87313702 0.48745939 0.00388303 -30.17217173
-0.00495763 0.00091434 0.99998729 28.21234402
Axis -0.00169999 0.00467995 0.99998760
Axis point 148.29094824 193.50022734 0.00000000
Rotation angle (degrees) 60.82700556
Shift along axis 27.65444012
> save /Users/uozumilab2/Desktop/image8.png supersample 3
> hide #!9 models
> show #!10 models
> fitmap #11 inMap #10
Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms
average map value = 0.0748, steps = 44
shifted from previous position = 0.327
rotated from previous position = 0.274 degrees
atoms outside contour = 14959, contour level = 0.09
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93259620 -0.36091339 -0.00242011 389.09830628
0.36089640 -0.93258945 0.00554036 274.00874153
-0.00425656 0.00429351 0.99998172 27.96526138
Axis -0.00172738 0.00254422 0.99999527
Axis point 168.99475196 173.30485046 0.00000000
Rotation angle (degrees) 158.84411601
Shift along axis 27.99014385
> save /Users/uozumilab2/Desktop/image9.png supersample 3
> hide #!10 models
> show #!1 models
> hide #11 models
> show #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A #11/B #11/C #11/D #12/A #12/B #12/C #12/D
Alignment identifier is 2
> select #11/A-D:511 #12/A-D:511
64 atoms, 56 bonds, 8 residues, 2 models selected
> select #11/A-D:511-519 #12/A-D:511-519
608 atoms, 600 bonds, 72 residues, 2 models selected
Potassium Channel GORK [ID: 2] region 8 chains [519-527] RMSD: 6.782
> color (#12 & sel) red
> select add #12
22248 atoms, 22760 bonds, 2740 residues, 2 models selected
> select add #11
43780 atoms, 44805 bonds, 5396 residues, 2 models selected
> select subtract #12
21836 atoms, 22345 bonds, 2692 residues, 1 model selected
> select subtract #11
Nothing selected
> fitmap #12 inMap #1
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J85_004_volume_map_sharp.mrc
(#1) using 21944 atoms
average map value = 0.07121, steps = 100
shifted from previous position = 0.462
rotated from previous position = 1.48 degrees
atoms outside contour = 14955, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.46720793 -0.88406548 0.01204087 248.68145727
0.88414676 0.46718147 -0.00509639 -27.42986720
-0.00111973 0.01302697 0.99991452 25.69845366
Axis 0.01024872 0.00744229 0.99991978
Axis point 147.14177537 192.29130247 0.00000000
Rotation angle (degrees) 62.15041770
Shift along axis 28.04091842
> turn x -90
> fitmap #12 inMap #1
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J85_004_volume_map_sharp.mrc
(#1) using 21944 atoms
average map value = 0.07121, steps = 120
shifted from previous position = 0.00565
rotated from previous position = 0.00152 degrees
atoms outside contour = 14953, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.46720047 -0.88406963 0.01202563 248.68717876
0.88415069 0.46717426 -0.00507631 -27.43182441
-0.00113025 0.01300413 0.99991480 25.70909608
Axis 0.01022440 0.00743959 0.99992005
Axis point 147.14626746 192.29364096 0.00000000
Rotation angle (degrees) 62.15088367
Shift along axis 28.04563662
> save /Users/uozumilab2/Desktop/image10.png supersample 3
> hide #!1 models
> show #!2 models
> fitmap #12 inMap #2
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J92_003_volume_map_sharp.mrc
(#2) using 21944 atoms
average map value = 0.05803, steps = 124
shifted from previous position = 0.648
rotated from previous position = 1.73 degrees
atoms outside contour = 9873, contour level = 0.05
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J92_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.73915103 -0.67353415 0.00273842 406.93546898
0.67353572 -0.73912652 0.00645135 194.08179893
-0.00232116 0.00661295 0.99997544 26.80555828
Axis 0.00011996 0.00375597 0.99999294
Axis point 165.90385242 175.78960718 0.00000000
Rotation angle (degrees) 137.65914874
Shift along axis 27.58315076
> save /Users/uozumilab2/Desktop/image11.png supersample 3
> hide #!2 models
> show #!3 models
> fitmap #12 inMap #3
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J93_004_volume_map_sharp.mrc
(#3) using 21944 atoms
average map value = 0.06628, steps = 88
shifted from previous position = 0.278
rotated from previous position = 0.328 degrees
atoms outside contour = 16154, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J93_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.08742467 -0.99615148 0.00625699 354.51215608
0.99616983 -0.08743300 -0.00106940 41.65531474
0.00161235 0.00613953 0.99997985 26.54050968
Axis 0.00361832 0.00233125 0.99999074
Axis point 158.15811125 183.13088179 0.00000000
Rotation angle (degrees) 95.01628656
Shift along axis 27.92011250
> save /Users/uozumilab2/Desktop/image12.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/uozumilab2/Desktop/image13.png supersample 3
> fitmap #12 inMap #4
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21944 atoms
average map value = 0.07184, steps = 2000
shifted from previous position = 0.54
rotated from previous position = 2.62 degrees
atoms outside contour = 15525, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.50293282 -0.86429959 0.00669356 240.69525495
0.86431505 0.50294975 0.00102354 -30.75045030
-0.00425117 0.00527057 0.99997707 27.64475099
Axis 0.00245684 0.00633136 0.99997694
Axis point 147.20375154 193.74787661 0.00000000
Rotation angle (degrees) 59.80597466
Shift along axis 28.04077089
> save /Users/uozumilab2/Desktop/image13.png supersample 3
> hide #!4 models
> show #!5 models
> fitmap #12 inMap #5
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21944 atoms
average map value = 0.07405, steps = 2000
shifted from previous position = 0.38
rotated from previous position = 0.46 degrees
atoms outside contour = 15311, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.17162995 -0.98510950 0.01012090 365.61365910
0.98516119 -0.17161289 0.00253717 56.03432857
-0.00076251 0.01040617 0.99994556 26.36568994
Axis 0.00399378 0.00552369 0.99997677
Axis point 159.26127505 181.61028305 0.00000000
Rotation angle (degrees) 99.88368829
Shift along axis 28.13477304
> save /Users/uozumilab2/Desktop/image14.png supersample 3
> hide #!5 models
> show #!6 models
> fitmap #12 inMap #6
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J87_012_volume_map_sharp.mrc
(#6) using 21944 atoms
average map value = 0.07811, steps = 2000
shifted from previous position = 0.457
rotated from previous position = 1.12 degrees
atoms outside contour = 15331, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J87_012_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.34777074 -0.93757586 0.00264782 386.79983897
0.93757837 -0.34776431 0.00260647 91.54528181
-0.00152295 0.00338899 0.99999310 27.39241129
Axis 0.00041731 0.00222422 0.99999744
Axis point 161.57376957 180.27752509 0.00000000
Rotation angle (degrees) 110.35103856
Shift along axis 27.75737279
> save /Users/uozumilab2/Desktop/image15.png supersample 3
> hide #!6 models
> show #!7 models
> fitmap #12 inMap #7
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J88_009_volume_map_sharp.mrc
(#7) using 21944 atoms
average map value = 0.07629, steps = 2000
shifted from previous position = 0.12
rotated from previous position = 3.81 degrees
atoms outside contour = 14967, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J88_009_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.54819789 -0.83634016 0.00377009 229.64803023
0.83634773 0.54819844 -0.00097848 -33.10891427
-0.00124841 0.00368951 0.99999241 27.39975913
Axis 0.00279069 0.00300023 0.99999161
Axis point 145.50808289 195.88823287 0.00000000
Rotation angle (degrees) 56.75677295
Shift along axis 27.94107077
> save /Users/uozumilab2/Desktop/image16.png supersample 3
> hide #!7 models
> show #!8 models
> fitmap #12 inMap #8
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J89_013_volume_map_sharp.mrc
(#8) using 21944 atoms
average map value = 0.07614, steps = 2000
shifted from previous position = 1.18
rotated from previous position = 4.27 degrees
atoms outside contour = 15422, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.20612135 0.97851575 -0.00457254 63.74864348
-0.97849527 -0.20607525 0.00894351 370.39223812
0.00780907 0.00631766 0.99994955 25.60633775
Axis -0.00134174 -0.00632667 -0.99997909
Axis point 182.03763380 159.27025069 0.00000000
Rotation angle (degrees) 101.89527713
Shift along axis -28.03468387
> save /Users/uozumilab2/Desktop/image17.png supersample 3
> hide #!8 models
> show #!9 models
> fitmap #12 inMap #9
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J90_011_volume_map_sharp.mrc
(#9) using 21944 atoms
average map value = 0.08055, steps = 2000
shifted from previous position = 0.845
rotated from previous position = 7.2 degrees
atoms outside contour = 14864, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
0.49723377 -0.86755629 0.01023045 241.74523457
0.86761293 0.49723143 -0.00295176 -29.98732725
-0.00252608 0.01034379 0.99994331 26.29190399
Axis 0.00766196 0.00735134 0.99994362
Axis point 146.82380141 193.31684751 0.00000000
Rotation angle (degrees) 60.18479327
Shift along axis 27.92221782
> save /Users/uozumilab2/Desktop/image18.png supersample 3
> hide #!9 models
> show #!10 models
> fitmap #12 inMap #10
Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21944 atoms
average map value = 0.06788, steps = 52
shifted from previous position = 0.202
rotated from previous position = 0.954 degrees
atoms outside contour = 15891, contour level = 0.09
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93330556 -0.35906053 0.00403379 387.88850244
0.35908314 -0.93324084 0.01099192 273.59329509
-0.00018227 0.01170729 0.99993145 26.04765414
Axis 0.00099612 0.00587067 0.99998227
Axis point 168.53851925 172.73999988 0.00000000
Rotation angle (degrees) 158.95640412
Shift along axis 28.03974965
> save /Users/uozumilab2/Desktop/image19.png supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,6
Model Number: MX2G3J/A
Chip: Apple M4 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 6日 17時間 37分
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 2 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 , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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