![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17684 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-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 0x00000001e35e1300 (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.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 58)
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{
"uptime" : 160000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 1679,
"osVersion" : {
"train" : "macOS 14.0",
"build" : "23A344",
"releaseType" : "User"
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"captureTime" : "2025-05-15 13:19:04.8660 +0800",
"codeSigningMonitor" : 1,
"incident" : "558603DA-2D1A-434A-994F-B0992DCA77D6",
"pid" : 48854,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-15 09:33:51.8977 +0800",
"procStartAbsTime" : 3693330667252,
"procExitAbsTime" : 4017634971236,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C774503C-C800-5360-88AA-F84C63372F7F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "11C288E1-C88C-2A08-8F01-07CD7707148E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 15066,
"sleepWakeUUID" : "EF087BC2-E254-457B-9B82-41640DD199EC",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 105553653137047\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":48854},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 105553653137047\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
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"uuid" : "8790ba20-19ec-3a36-8975-e34382d9747c",
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"base" : 6647422976,
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"CFBundleIdentifier" : "com.apple.CoreFoundation",
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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},
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"path" : "\/System\/Library\/PrivateFrameworks\/CalendarDatabase.framework\/Versions\/A\/CalendarDatabase",
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=5.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 2896K 76 \nCG raster data 400K 8 \nColorSync 656K 31 \nCoreAnimation 5376K 236 \nCoreGraphics 48K 3 \nCoreImage 80K 5 \nCoreServices 624K 2 \nCoreUI image data 5680K 61 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.6G 159 \nMALLOC guard page 192K 12 \nMach message 96K 6 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 200.3M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 338.5M 368 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 3239K 548 \n__AUTH_CONST 40.1M 810 \n__CTF 824 1 \n__DATA 26.2M 961 \n__DATA_CONST 50.1M 971 \n__DATA_DIRTY 2888K 320 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 916.5M 155 \n__OBJC_RO 70.6M 1 \n__OBJC_RW 2153K 1 \n__TEXT 1.1G 989 \ndyld private memory 592K 5 \nmapped file 607.3M 140 \nshared memory 3312K 32 \n=========== ======= ======= \nTOTAL 8.0G 5996 \nTOTAL, minus reserved VM space 7.9G 5996 \n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/ChimeraX/D398.cxs
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened P34_J608_004.cmap as #5, grid size 256,256,256, pixel 0.932, shown at
level 0.506, step 1, values float32
Opened P49_J393_003.cmap as #6, grid size 256,256,256, pixel 0.932, shown at
level 0.411, step 1, values float32
Opened P34_J1433.cmap as #7, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 0 as #9.1, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 1 as #9.2, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 2 as #9.3, grid size
256,256,256, pixel 0.932, shown at level 0.562, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 3 as #9.4, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened P34_J608_004.cmap 0 as #10.1, grid size 256,256,256, pixel 0.932, shown
at level 0.506, step 1, values float32
Opened P34_J608_004.cmap 1 as #10.2, grid size 256,256,256, pixel 0.932, shown
at level 0.506, step 1, values float32
Opened P34_J608_004.cmap 2 as #10.3, grid size 256,256,256, pixel 0.932, shown
at level 0.362, step 1, values float32
Opened P49_J393_003.cmap 0 as #11.1, grid size 256,256,256, pixel 0.932, shown
at level 0.411, step 1, values float32
Opened P49_J393_003.cmap 1 as #11.2, grid size 256,256,256, pixel 0.932, shown
at level 0.411, step 1, values float32
Opened P49_J393_003.cmap 2 as #11.3, grid size 256,256,256, pixel 0.932, shown
at level 0.201, step 1, values float32
Opened P34_J1433.cmap 0 as #12.1, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 1 as #12.2, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 2 as #12.3, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 3 as #12.4, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 4 as #12.5, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 5 as #12.6, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 0 as #13.1, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 1 as #13.2, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 2 as #13.3, grid size 256,256,256, pixel 0.932, shown at
level 0.157, step 1, values float32
Opened P34_J1433.cmap 3 as #13.4, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Log from Wed Dec 11 15:01:23 2024 Startup Messages
---
warnings | Data format provider 'LAMMPS coordinates' supplied unknown keywords with format description: {'default_for': '.data'}
Data format provider 'LAMMPS trajectory' supplied unknown keywords with format
description: {'default_for': '.dump'}
Data format provider 'LAMMPS coordinates' supplied unknown keywords with
format description: {'default_for': '.data'}
Data format provider 'LAMMPS trajectory' supplied unknown keywords with format
description: {'default_for': '.dump'}
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:/183/183-map/183-0708-PDB/ACh/ACh-cryosparc_P34_J1670_map_2.72.mrc
Opened ACh-cryosparc_P34_J1670_map_2.72.mrc as #1, grid size 256,256,256,
pixel 0.932, shown at level 0.189, step 1, values float32
> open "D:/183/183-map/183-0708-PDB/ACh/VAChT-ACh -all.pdb"
Chain information for VAChT-ACh -all.pdb #2
---
Chain | Description
A | No description available
> volume #1 level 0.6025
> set bgColor white
> open D:/183/183-map/183-0708-PDB/apo/apo-
> cryosparc_P34_J608_004_volume_map_sharp-resample.mrc
Opened apo-cryosparc_P34_J608_004_volume_map_sharp-resample.mrc as #3, grid
size 256,256,256, pixel 0.932, shown at level 0.195, step 1, values float32
> open D:/183/183-map/183-0708-PDB/apo/VAChT-apo.pdb
Chain information for VAChT-apo.pdb #4
---
Chain | Description
B | No description available
> volume #3 level 0.4207
> open "D:/183/183-map/183-0708-PDB/ph=5.5/vop resample-918-3.3-ph5.5.mrc"
Opened vop resample-918-3.3-ph5.5.mrc as #5, grid size 256,256,256, pixel
0.932, shown at level 0.151, step 1, values float32
> open D:/183/183-map/183-0708-PDB/ph=5.5/0813-apo-coot-13.pdb
Chain information for 0813-apo-coot-13.pdb #6
---
Chain | Description
A | No description available
> volume #5 level 0.3406
> open D:/183/183-map/183-0708-PDB/vesamicol/Vesamicol-
> cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc
Opened Vesamicol-cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc as #7,
grid size 256,256,256, pixel 0.932, shown at level 0.0508, step 1, values
float32
> open D:/183/183-map/183-0708-PDB/vesamicol/0812-VSM.pdb
Chain information for 0812-VSM.pdb #8
---
Chain | Description
A | No description available
> volume #5 level 0.6636
> volume #7 level 0.3121
> cartoon style width 0.7
> transparency 60 cartoons
> hide #!8 models
> show #!8 models
> hide #!6 models
> hide #!4 models
> hide #!2 models
> hide #!8 models
> show #!8 models
> close #8
> open D:/183/183-map/183-0708-PDB/vesamicol/pdb-load/vsm_PDB-coot-0.pdb
Chain information for vsm_PDB-coot-0.pdb #8
---
Chain | Description
A | No description available
> close #8
> open D:/183/183-map/183-0708-PDB/vesamicol/pdb-load/vsm_PDB.pdb
Chain information for vsm_PDB.pdb #8
---
Chain | Description
A | No description available
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> select add #6
3037 atoms, 3112 bonds, 1 pseudobond, 404 residues, 2 models selected
> select subtract #6
Nothing selected
> select add #8
3068 atoms, 3146 bonds, 1 pseudobond, 406 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.98754,-0.10604,-0.11624,24.986,0.1012,0.99376,-0.046825,-4.9074,0.12048,0.034479,0.99212,-15.408
> view matrix models
> #8,-0.96306,0.2136,-0.16397,201.68,-0.22098,-0.27893,0.93454,55.656,0.15388,0.93626,0.31583,-39.911
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.96306,0.2136,-0.16397,217.04,-0.22098,-0.27893,0.93454,64.528,0.15388,0.93626,0.31583,-35.804
> color #6 #00aaff66
> cartoon style width 2
> select add #6
6105 atoms, 6258 bonds, 2 pseudobonds, 810 residues, 4 models selected
> view matrix models
> #6,1,0,0,12.821,0,1,0,-7.4184,0,0,1,4.2268,#8,-0.96306,0.2136,-0.16397,229.86,-0.22098,-0.27893,0.93454,57.11,0.15388,0.93626,0.31583,-31.578
> view matrix models
> #6,1,0,0,7.2454,0,1,0,-4.4674,0,0,1,3.2543,#8,-0.96306,0.2136,-0.16397,224.28,-0.22098,-0.27893,0.93454,60.061,0.15388,0.93626,0.31583,-32.55
> select subtract #8
3037 atoms, 3112 bonds, 1 pseudobond, 404 residues, 2 models selected
> select subtract #6
Nothing selected
> select add #8
3068 atoms, 3146 bonds, 1 pseudobond, 406 residues, 2 models selected
> view matrix models
> #8,-0.96306,0.2136,-0.16397,181.78,-0.22098,-0.27893,0.93454,68.798,0.15388,0.93626,0.31583,-56.806
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.97565,0.088717,-0.20059,200.13,-0.17507,-0.86592,0.46854,175.82,-0.13213,0.49225,0.86037,-39.339
> view matrix models
> #8,-0.88548,0.0056539,-0.46464,227.94,0.34126,-0.67073,-0.65853,223.27,-0.31537,-0.74168,0.59199,137.97
> view matrix models
> #8,-0.95761,-0.21089,-0.19624,229.08,0.28585,-0.61124,-0.73802,231.48,0.035694,-0.76283,0.64561,97.486
> view matrix models
> #8,-0.93496,0.23324,-0.26728,187.97,0.27583,0.95178,-0.13431,3.7536,0.22307,-0.1993,-0.95421,192.21
> hide #!6 models
> show #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.93052,0.228,-0.2866,190.14,0.27476,0.95203,-0.13472,3.8846,0.24214,-0.20411,-0.94853,190.1
> view matrix models
> #8,-0.94206,0.24257,-0.23169,183.88,0.27781,0.9513,-0.13361,3.5205,0.18799,-0.19024,-0.96357,195.96
> view matrix models
> #8,-0.92605,0.22303,-0.30445,192.13,0.27377,0.95226,-0.13512,4.0084,0.25978,-0.20848,-0.9429,188.09
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.92605,0.22303,-0.30445,231.05,0.27377,0.95226,-0.13512,2.8097,0.25978,-0.20848,-0.9429,212.04
> hide #!2 models
> show #!7 models
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule vsm_PDB.pdb (#8) to map Vesamicol-
cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) using 3068 atoms
average map value = 0.05745, steps = 112
shifted from previous position = 2.29
rotated from previous position = 7.01 degrees
atoms outside contour = 2590, contour level = 0.31205
Position of vsm_PDB.pdb (#8) relative to Vesamicol-
cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) coordinates:
Matrix rotation and translation
-0.94874131 0.11842422 -0.29302837 244.09970759
0.18793346 0.95681279 -0.22178886 18.65504729
0.25410812 -0.26549009 -0.93002370 217.73038409
Axis -0.07898820 -0.98892703 0.12563513
Axis point 105.68249952 0.00000000 127.40186397
Rotation angle (degrees) 163.94074284
Shift along axis -10.37489195
> view matrix models
> #8,-0.94874,0.11842,-0.29303,246.22,0.18793,0.95681,-0.22179,20.676,0.25411,-0.26549,-0.93002,217.19
> view matrix models
> #8,-0.94874,0.11842,-0.29303,242.88,0.18793,0.95681,-0.22179,25.536,0.25411,-0.26549,-0.93002,217.82
> view matrix models
> #8,-0.94874,0.11842,-0.29303,242.54,0.18793,0.95681,-0.22179,26.911,0.25411,-0.26549,-0.93002,217.88
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.94935,-0.25082,-0.18927,269.96,-0.19304,0.94083,-0.27851,74.751,0.24792,-0.22787,-0.9416,215.85
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.94935,-0.25082,-0.18927,268.11,-0.19304,0.94083,-0.27851,70.575,0.24792,-0.22787,-0.9416,215.97
> fitmap #8 inMap #7
Fit molecule vsm_PDB.pdb (#8) to map Vesamicol-
cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) using 3068 atoms
average map value = 0.07904, steps = 84
shifted from previous position = 3.85
rotated from previous position = 6.69 degrees
atoms outside contour = 2470, contour level = 0.31205
Position of vsm_PDB.pdb (#8) relative to Vesamicol-
cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) coordinates:
Matrix rotation and translation
-0.96836724 -0.13735439 -0.20832344 259.30112099
-0.08221532 0.96387571 -0.25334611 52.58553585
0.23559611 -0.22820470 -0.94467830 221.11939410
Axis 0.05611462 -0.99081046 0.12306816
Axis point 118.40737724 0.00000000 128.70411903
Rotation angle (degrees) 167.05483683
Shift along axis -10.33895784
> show #!6 models
> hide #!6 models
> close session
> open D:/183/183-map/183-0708-PDB/ACh/PDB-
> load/cryosparc_P34_J1741_003_volume_map_sharp.mrc
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.932, shown at level 0.197, step 1, values float32
> open D:/183/183-map/183-0708-PDB/apo/pdb-
> load/cryosparc_P34_J608_004_volume_map_sharp.mrc
Opened cryosparc_P34_J608_004_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.932, shown at level 0.206, step 1, values float32
> open
> "D:/183/183-map/183-0708-PDB/ph=5.5/map/cryosparc_P49_J393_003_volume_map_sharp
> (1).mrc"
Opened cryosparc_P49_J393_003_volume_map_sharp (1).mrc as #3, grid size
256,256,256, pixel 0.932, shown at level 0.158, step 1, values float32
> open D:/183/183-map/183-0708-PDB/vesamicol/pdb-
> load/cryosparc_P34_J1433_map.mrc
Opened cryosparc_P34_J1433_map.mrc as #4, grid size 256,256,256, pixel 0.832,
shown at level 0.0676, step 1, values float32
> volume #1 level 0.496
> set bgColor white
> volume #2 level 0.5064
> surface dust #1 size 9.32
> surface dust #2 size 9.32
> select add #2
2 models selected
> view matrix models #2,1,0,0,20.482,0,1,0,-46.786,0,0,1,37.321
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.094748,0.83461,-0.54264,123.48,-0.65155,0.36014,0.66767,22.631,0.75267,0.41682,0.50966,-40.567
> view matrix models
> #2,-0.86557,0.077572,-0.49474,303.35,0.14261,-0.90884,-0.39201,220.3,-0.48005,-0.40987,0.77561,175.32
> view matrix models
> #2,-0.5224,-0.52055,-0.67537,358.32,0.53062,0.42154,-0.73535,56.031,0.66749,-0.74251,0.056002,170.97
> view matrix models
> #2,-0.47041,-0.74359,-0.47516,352.81,0.42102,0.2841,-0.86141,102.74,0.77553,-0.60527,0.17943,124.81
> view matrix models
> #2,-0.52097,-0.53275,-0.66691,358.51,0.52505,0.41601,-0.74247,58.322,0.67299,-0.73697,0.062988,168.7
> view matrix models
> #2,-0.50307,-0.63615,-0.58501,358.16,0.47607,0.36097,-0.80191,78.829,0.7213,-0.68192,0.12126,148.43
> view matrix models
> #2,-0.7816,-0.36302,-0.50727,348.52,0.61437,-0.58872,-0.52531,141.38,-0.10794,-0.72224,0.68317,180.29
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.7816,-0.36302,-0.50727,311.3,0.61437,-0.58872,-0.52531,175.96,-0.10794,-0.72224,0.68317,138.52
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map cryosparc_P34_J608_004_volume_map_sharp.mrc in map
cryosparc_P34_J1741_003_volume_map_sharp.mrc using 31893 points
correlation = 0.9112, correlation about mean = 0.7477, overlap = 3.049e+04
steps = 196, shift = 1.76, angle = 19.9 degrees
Position of cryosparc_P34_J608_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.83713208 -0.29889581 -0.45811698 305.77226424
0.46846477 -0.82413718 -0.31833735 197.17935390
-0.28240154 -0.48110208 0.82993383 112.33118092
Axis -0.20247587 -0.21858629 0.95458030
Axis point 143.07630505 145.10430188 0.00000000
Rotation angle (degrees) 156.30073024
Shift along axis 2.21692267
> select up
8 models selected
> select up
8 models selected
> select up
8 models selected
> select up
8 models selected
> select up
8 models selected
> vop resample #2 on #1
Opened cryosparc_P34_J608_004_volume_map_sharp.mrc resampled as #5, grid size
256,256,256, pixel 0.932, shown at step 1, values float32
> select subtract #2
6 models selected
> show #!3 models
> select subtract #3
4 models selected
> select subtract #1
2 models selected
> select add #3
4 models selected
> volume #3 level 0.6321
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.029785,-0.67333,-0.73874,292.35,0.74268,0.47974,-0.46721,32.197,0.66899,-0.56256,0.48578,51.695,#4,-0.029785,-0.67333,-0.73874,292.35,0.74268,0.47974,-0.46721,32.197,0.66899,-0.56256,0.48578,51.695
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.029785,-0.67333,-0.73874,284.81,0.74268,0.47974,-0.46721,27.055,0.66899,-0.56256,0.48578,59.37,#4,-0.029785,-0.67333,-0.73874,284.81,0.74268,0.47974,-0.46721,27.055,0.66899,-0.56256,0.48578,59.37
> view matrix models
> #3,-0.029785,-0.67333,-0.73874,281.85,0.74268,0.47974,-0.46721,22.055,0.66899,-0.56256,0.48578,52.201,#4,-0.029785,-0.67333,-0.73874,281.85,0.74268,0.47974,-0.46721,22.055,0.66899,-0.56256,0.48578,52.201
> fitmap #3 inMap #1
Fit map cryosparc_P49_J393_003_volume_map_sharp (1).mrc in map
cryosparc_P34_J1741_003_volume_map_sharp.mrc using 16359 points
correlation = 0.79, correlation about mean = 0.2221, overlap = 1.446e+04
steps = 192, shift = 3.17, angle = 16.8 degrees
Position of cryosparc_P49_J393_003_volume_map_sharp (1).mrc (#3) relative to
cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.16852532 -0.75346085 -0.63552810 297.54505780
0.85396218 0.21040500 -0.47589740 41.19435297
0.49228835 -0.62291772 0.60796850 68.75817511
Axis -0.07466334 -0.57275445 0.81631962
Axis point 127.74312162 197.81308472 0.00000000
Rotation angle (degrees) 100.08307567
Shift along axis 10.31869008
> vop resample #3 on #1
Opened cryosparc_P49_J393_003_volume_map_sharp (1).mrc resampled as #6, grid
size 256,256,256, pixel 0.932, shown at step 1, values float32
> select subtract #3
2 models selected
> show #!4 models
[Repeated 1 time(s)]
> volume #4 level 0.1923
> surface dust #4 size 8.32
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.029785,-0.67333,-0.73874,287.41,0.74268,0.47974,-0.46721,-14.615,0.66899,-0.56256,0.48578,70.211
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.91428,-0.031959,-0.40383,277.12,-0.37323,0.45398,0.80908,-31.138,0.15747,0.89044,-0.42699,68.847
> view matrix models
> #4,-0.9563,-0.034336,-0.29035,269.75,-0.26678,0.50883,0.81849,-48.825,0.11964,0.86018,-0.49576,83.149
> view matrix models
> #4,-0.91672,-0.04379,-0.39712,277.9,-0.35542,0.54338,0.76054,-37.123,0.18248,0.83835,-0.51369,80.802
> view matrix models
> #4,-0.93865,-0.060616,-0.33951,275.83,-0.31457,0.55402,0.77078,-43.532,0.14137,0.8303,-0.53909,88.569
> volume #4 level 0.425
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.93865,-0.060616,-0.33951,258.61,-0.31457,0.55402,0.77078,-12.394,0.14137,0.8303,-0.53909,57.353
> view matrix models
> #4,-0.93865,-0.060616,-0.33951,265.15,-0.31457,0.55402,0.77078,4.0027,0.14137,0.8303,-0.53909,69.037
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.90105,0.23003,-0.3677,233.37,-0.14251,0.64368,0.75191,-21.309,0.40964,0.7299,-0.5472,52.825
> view matrix models
> #4,-0.90467,0.19049,-0.38117,239.41,-0.14777,0.69878,0.69991,-21.005,0.39968,0.68951,-0.60401,64.298
> view matrix models
> #4,-0.95741,0.23545,-0.1671,216.94,0.046821,0.69772,0.71484,-42.651,0.2849,0.67657,-0.67903,85.67
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.95741,0.23545,-0.1671,214.18,0.046821,0.69772,0.71484,-39.896,0.2849,0.67657,-0.67903,84.657
> fitmap #4 inMap #1
Fit map cryosparc_P34_J1433_map.mrc in map
cryosparc_P34_J1741_003_volume_map_sharp.mrc using 17649 points
correlation = 0.2908, correlation about mean = 0.06262, overlap = 2848
steps = 72, shift = 2.4, angle = 9.3 degrees
Position of cryosparc_P34_J1433_map.mrc (#4) relative to
cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.91745885 0.36902847 -0.14861776 192.17749894
0.17815932 0.71513397 0.67590137 -52.76296656
0.35570846 0.59363406 -0.72185185 90.18932965
Axis -0.15081752 -0.92456199 -0.34991312
Axis point 93.92171649 0.00000000 69.39230268
Rotation angle (degrees) 164.17274590
Shift along axis -11.75953063
> view matrix models
> #4,-0.91746,0.36903,-0.14862,171.35,0.17816,0.71513,0.6759,-70.702,0.35571,0.59363,-0.72185,54.044
> view matrix models
> #4,-0.91746,0.36903,-0.14862,190.65,0.17816,0.71513,0.6759,-70.254,0.35571,0.59363,-0.72185,100.94
> view matrix models
> #4,-0.91746,0.36903,-0.14862,188.59,0.17816,0.71513,0.6759,-48.086,0.35571,0.59363,-0.72185,93.477
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.93434,0.12817,-0.33253,235.85,-0.082841,0.82941,0.55246,-19.879,0.34661,0.54374,-0.76434,104.32
> fitmap #4 inMap #1
Fit map cryosparc_P34_J1433_map.mrc in map
cryosparc_P34_J1741_003_volume_map_sharp.mrc using 17649 points
correlation = 0.2888, correlation about mean = 0.06942, overlap = 2867
steps = 76, shift = 2.61, angle = 11.9 degrees
Position of cryosparc_P34_J1433_map.mrc (#4) relative to
cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.95494352 -0.04967564 -0.29260076 252.06811138
-0.22095432 0.77721510 0.58916540 -2.89213908
0.19814657 0.62727108 -0.75317257 107.40790143
Axis 0.07311522 -0.94162065 -0.32864071
Axis point 118.68733729 0.00000000 72.02751855
Rotation angle (degrees) 164.89513190
Shift along axis -14.14529510
> view matrix models
> #4,-0.95134,-0.13079,-0.27902,258.86,-0.24192,0.87783,0.41338,7.5809,0.19087,0.46076,-0.86676,138.16
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.95134,-0.13079,-0.27902,265.02,-0.24192,0.87783,0.41338,7.2592,0.19087,0.46076,-0.86676,139.78
> fitmap #4 inMap #1
Fit map cryosparc_P34_J1433_map.mrc in map
cryosparc_P34_J1741_003_volume_map_sharp.mrc using 17649 points
correlation = 0.9282, correlation about mean = 0.5568, overlap = 1.668e+04
steps = 76, shift = 1.06, angle = 10.2 degrees
Position of cryosparc_P34_J1433_map.mrc (#4) relative to
cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.97578855 -0.12798227 -0.17736188 256.23520117
-0.17652228 0.93963163 0.29314208 6.75126103
0.12913785 0.31735301 -0.93947351 170.29463811
Axis 0.07778298 -0.98469833 -0.15594554
Axis point 121.69653961 0.00000000 94.84030557
Rotation angle (degrees) 171.04658942
Shift along axis -13.27390718
> vop resample #4 on #1
Opened cryosparc_P34_J1433_map.mrc resampled as #7, grid size 256,256,256,
pixel 0.932, shown at step 1, values float32
> show #!6 models
> show #!5 models
> close #4
> close #3
> close #2
> hide #!1 models
> hide #!7 models
> hide #!6 models
> save D:/183/183-map/P34_J608_004.cmap models #5
> hide #!5 models
> show #!6 models
> save D:/183/183-map/P49_J393_003.cmap models #6
> save D:/183/183-map/P34_J1433.cmap models #7
> hide #!6 models
> show #!6 models
> show #!5 models
> show #!1 models
> show #!7 models
> open D:/183/183-map/183-0708-PDB/ACh/PDB-load/ACh.pdb
Chain information for ACh.pdb #2
---
Chain | Description
A | No description available
> hide #!7 models
> hide #!6 models
> hide #!5 models
> volume #1 level 0.7931
> open D:/183/183-map/183-0708-PDB/apo/pdb-load/apo-load.pdb
Chain information for apo-load.pdb #3
---
Chain | Description
B | No description available
> select add #3
3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,8.7726,0,1,0,-21.367,0,0,1,52.877
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.75698,-0.28042,0.5902,3.5159,0.22978,0.95978,0.16131,-61.552,-0.6117,0.013504,0.79097,146.02
> view matrix models
> #3,0.74118,-0.28903,0.6059,4.5978,0.23509,0.95717,0.16901,-62.73,-0.62879,0.017171,0.77738,149.11
> view matrix models
> #3,0.78823,-0.26995,0.553,2.844,0.21733,0.96285,0.16024,-60.346,-0.57572,-0.0061199,0.81762,141.14
> view matrix models
> #3,0.53617,-0.34298,0.77129,16.139,0.29281,0.93257,0.21114,-71.294,-0.7917,0.11263,0.60044,176.76
> view matrix models
> #3,0.58816,-0.33278,0.73711,12.747,0.28051,0.93878,0.19999,-69.339,-0.75854,0.089139,0.64551,170.59
> view matrix models
> #3,0.5765,-0.33524,0.74516,13.484,0.28339,0.93739,0.20247,-69.789,-0.76638,0.094442,0.63541,172.01
> view matrix models
> #3,0.45349,-0.35545,0.81731,22.032,0.30983,0.92271,0.22938,-74.168,-0.83567,0.14921,0.52857,185.67
> view matrix models
> #3,0.252,0.42176,-0.87099,144.29,-0.19263,0.90388,0.38195,-30.734,0.94836,0.071525,0.30902,12.14
> view matrix models
> #3,-0.98929,0.061172,-0.1325,247.86,-0.02639,-0.96793,-0.24983,242.22,-0.14353,-0.24366,0.95918,102.94
> view matrix models
> #3,-0.79274,0.029604,-0.60884,282.5,0.095093,-0.98058,-0.1715,220.74,-0.60209,-0.19385,0.77454,171.23
> view matrix models
> #3,-0.80749,0.02986,-0.58913,281.96,0.092136,-0.98008,-0.17596,221.53,-0.58265,-0.19637,0.78865,167.68
> view matrix models
> #3,-0.75795,0.028801,-0.65168,283.38,0.10132,-0.9817,-0.16123,218.99,-0.6444,-0.18823,0.74116,179.26
> view matrix models
> #3,-0.72146,0.027703,-0.6919,283.81,0.10688,-0.98277,-0.15079,217.29,-0.68416,-0.18274,0.70607,187.19
> hide #!2 models
> show #!5 models
> view matrix models
> #3,-0.74726,0.028504,-0.66392,283.55,0.10304,-0.98203,-0.15813,218.48,-0.6565,-0.18658,0.73089,181.63
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.74726,0.028504,-0.66392,278.75,0.10304,-0.98203,-0.15813,229.43,-0.6565,-0.18658,0.73089,131.19
> color #3 #55aa00ff
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.74763,-0.10139,-0.65633,293.27,0.18929,-0.97982,-0.064266,208.54,-0.63657,-0.17228,0.75173,124.84
> view matrix models
> #3,-0.74341,-0.12804,-0.65647,295.94,0.21334,-0.97563,-0.051306,203.79,-0.6339,-0.17819,0.75261,125.12
> view matrix models
> #3,-0.81666,-0.1209,-0.56432,293.21,0.18895,-0.97993,-0.063509,208.51,-0.54532,-0.15849,0.82311,104.54
> view matrix models
> #3,-0.80403,-0.14102,-0.57762,295.62,0.25877,-0.95763,-0.12641,204.86,-0.53533,-0.25111,0.80646,116.19
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.80403,-0.14102,-0.57762,296.02,0.25877,-0.95763,-0.12641,214.86,-0.53533,-0.25111,0.80646,119.09
> view matrix models
> #3,-0.80403,-0.14102,-0.57762,294.47,0.25877,-0.95763,-0.12641,216.07,-0.53533,-0.25111,0.80646,118.03
> fitmap #3 inMap #5
Fit molecule apo-load.pdb (#3) to map P34_J608_004.cmap (#5) using 3044 atoms
average map value = 0.8206, steps = 96
shifted from previous position = 2.15
rotated from previous position = 20.6 degrees
atoms outside contour = 969, contour level = 0.50641
Position of apo-load.pdb (#3) relative to P34_J608_004.cmap (#5) coordinates:
Matrix rotation and translation
-0.83705225 -0.29874831 -0.45835902 305.78501903
0.46848580 -0.82409338 -0.31841981 197.18691120
-0.28260325 -0.48126870 0.82976855 112.38139756
Axis -0.20260449 -0.21866225 0.95453562
Axis point 143.09744626 145.11722752 0.00000000
Rotation angle (degrees) 156.30369810
Shift along axis 2.20129557
> save D:/183/183-map/apo_load_resample.pdb models #3 relModel #5
> hide #!3 models
> hide #!5 models
> open D:/183/183-map/183-0708-PDB/ph=5.5/map/VAChT-protonated-pdb-load-
> coot-0.pdb
Chain information for VAChT-protonated-pdb-load-coot-0.pdb #4
---
Chain | Description
A | No description available
> show #!6 models
> select subtract #3
Nothing selected
> volume #6 level 0.411
> select add #4
3037 atoms, 3113 bonds, 1 pseudobond, 404 residues, 2 models selected
> view matrix models #4,1,0,0,-27.529,0,1,0,-0.11174,0,0,1,-37.184
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.62109,-0.61849,0.48138,43.099,0.15746,0.70015,0.69641,-54.599,-0.76776,-0.35673,0.53225,146.39
> view matrix models
> #4,0.32015,-0.84241,0.43341,111.26,0.015235,0.46201,0.88675,-28.358,-0.94725,-0.27729,0.16074,196.65
> view matrix models
> #4,0.20471,-0.063766,-0.97674,176.43,-0.90387,0.37066,-0.21363,206.55,0.37566,0.92658,0.018241,-93.059
> view matrix models
> #4,0.17988,-0.082537,-0.98022,182.04,-0.9153,0.35101,-0.19753,208.64,0.36037,0.93273,-0.012405,-88.806
> view matrix models
> #4,0.16446,-0.094534,-0.98184,185.51,-0.92207,0.33881,-0.18707,209.85,0.35034,0.9361,-0.031448,-86.044
> view matrix models
> #4,0.13682,-0.11669,-0.9837,191.7,-0.93355,0.31693,-0.16744,211.85,0.3313,0.94124,-0.065571,-80.861
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.13682,-0.11669,-0.9837,224.98,-0.93355,0.31693,-0.16744,208.33,0.3313,0.94124,-0.065571,-30.014
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.26413,-0.1403,-0.95423,209.46,-0.83692,-0.52508,-0.15446,296.76,-0.47937,0.83941,-0.25611,99.516
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.26413,-0.1403,-0.95423,209,-0.83692,-0.52508,-0.15446,298.75,-0.47937,0.83941,-0.25611,95.697
> view matrix models
> #4,0.26413,-0.1403,-0.95423,209.88,-0.83692,-0.52508,-0.15446,295.35,-0.47937,0.83941,-0.25611,96.287
> hide #!6 models
> show #!2 models
> view matrix models
> #4,0.26413,-0.1403,-0.95423,209.65,-0.83692,-0.52508,-0.15446,295.39,-0.47937,0.83941,-0.25611,96.044
> view matrix models
> #4,0.26413,-0.1403,-0.95423,225.68,-0.83692,-0.52508,-0.15446,278.34,-0.47937,0.83941,-0.25611,137.44
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.69298,-0.67158,-0.26224,333.8,0.44318,-0.10991,-0.88967,149.74,0.56866,-0.73274,0.3738,135.74
> view matrix models
> #4,-0.30101,-0.8057,-0.51014,328.23,0.68458,0.18985,-0.70378,65.432,0.66388,-0.56108,0.49442,91.182
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.30101,-0.8057,-0.51014,308.58,0.68458,0.18985,-0.70378,78.098,0.66388,-0.56108,0.49442,51.289
> hide #!2 models
> show #!6 models
> view matrix models
> #4,-0.30101,-0.8057,-0.51014,309.84,0.68458,0.18985,-0.70378,79.468,0.66388,-0.56108,0.49442,50.628
> fitmap #4 inMap #6
Fit molecule VAChT-protonated-pdb-load-coot-0.pdb (#4) to map
P49_J393_003.cmap (#6) using 3037 atoms
average map value = 0.1468, steps = 64
shifted from previous position = 2.47
rotated from previous position = 5.59 degrees
atoms outside contour = 2510, contour level = 0.41095
Position of VAChT-protonated-pdb-load-coot-0.pdb (#4) relative to
P49_J393_003.cmap (#6) coordinates:
Matrix rotation and translation
-0.36106779 -0.79055386 -0.49462570 312.64698351
0.61854843 0.19390506 -0.76144508 94.52474795
0.69787379 -0.58088327 0.41898299 55.24191200
Axis 0.09734919 -0.64293144 0.75971199
Axis point 107.47552857 209.00945863 0.00000000
Rotation angle (degrees) 111.96807303
Shift along axis 11.63094219
> view matrix models
> #4,-0.36107,-0.79055,-0.49463,308.94,0.61855,0.19391,-0.76145,101.66,0.69787,-0.58088,0.41898,60.128
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.41125,-0.70842,-0.57361,313.22,0.662,0.20047,-0.7222,91.604,0.62661,-0.67673,0.38653,83.596
> view matrix models
> #4,-0.42352,-0.6846,-0.59326,313.85,0.67645,0.19659,-0.70977,89.051,0.60253,-0.70191,0.37983,90.218
> fitmap #4 inMap #6
Fit molecule VAChT-protonated-pdb-load-coot-0.pdb (#4) to map
P49_J393_003.cmap (#6) using 3037 atoms
average map value = 0.5124, steps = 104
shifted from previous position = 2.75
rotated from previous position = 19.4 degrees
atoms outside contour = 1293, contour level = 0.41095
Position of VAChT-protonated-pdb-load-coot-0.pdb (#4) relative to
P49_J393_003.cmap (#6) coordinates:
Matrix rotation and translation
-0.16866597 -0.75332040 -0.63565722 297.57781562
0.85351249 0.21094551 -0.47646444 41.25930084
0.49301944 -0.62290474 0.60738906 68.72269841
Axis -0.07436999 -0.57320062 0.81603318
Axis point 127.71038967 197.91443513 0.00000000
Rotation angle (degrees) 100.08830132
Shift along axis 10.29928726
> save D:/183/183-map/VAChT-protonated-resample.pdb models #4 relModel #6
> hide #!6 models
> hide #!4 models
> open D:/183/183-map/183-0708-PDB/vesamicol/pdb-load/vsm_PDB-coot-0.pdb
Chain information for vsm_PDB-coot-0.pdb #8
---
Chain | Description
A | No description available
> select subtract #4
Nothing selected
> select add #8
3068 atoms, 3146 bonds, 1 pseudobond, 406 residues, 2 models selected
> show #!4 models
> view matrix models
> #8,0.5645,0.81594,-0.12483,-32.77,-0.72929,0.42218,-0.53843,213.27,-0.38662,0.39498,0.83337,16.336
> view matrix models
> #8,0.75213,-0.49354,-0.43671,134.42,-0.57138,-0.1582,-0.80529,291.58,0.32836,0.85522,-0.40098,1.6301
> view matrix models
> #8,0.48994,-0.54596,-0.67962,197.47,-0.78762,0.056921,-0.61353,272.06,0.37365,0.83588,-0.40212,-1.3993
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.48994,-0.54596,-0.67962,197.16,-0.78762,0.056921,-0.61353,273.23,0.37365,0.83588,-0.40212,12.425
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.47583,-0.54708,-0.68869,199.94,-0.79388,0.069922,-0.60405,271.45,0.37862,0.83416,-0.40104,11.92
> view matrix models
> #8,0.55104,-0.41446,-0.72428,178.54,-0.83228,-0.33598,-0.44094,308.18,-0.060587,0.84578,-0.53008,76.921
> view matrix models
> #8,0.36721,-0.55118,-0.74924,219.81,-0.92246,-0.11255,-0.36931,284.79,0.11923,0.82676,-0.54977,59.499
> view matrix models
> #8,0.36426,-0.53876,-0.75964,219.74,-0.92825,-0.14417,-0.34287,286.58,0.075209,0.83003,-0.55262,64.721
> view matrix models
> #8,0.40609,-0.53965,-0.73748,212.51,-0.90767,-0.14459,-0.394,289.41,0.10599,0.82938,-0.54854,60.657
> hide #!4 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #8,0.279,-0.77586,-0.56586,238.64,-0.93904,-0.097153,-0.32979,280.87,0.20089,0.62338,-0.75567,95.34
> view matrix models
> #8,-0.049499,-0.71813,-0.69414,284.63,0.47218,0.5956,-0.64985,59.761,0.88011,-0.35993,0.30961,21.901
> view matrix models
> #8,-0.094297,-0.73324,-0.6734,289.73,0.68114,0.44579,-0.58079,45.424,0.72605,-0.51345,0.4574,43.794
> hide #!4 models
> show #!7 models
> fitmap #8 inMap #7
Fit molecule vsm_PDB-coot-0.pdb (#8) to map P34_J1433.cmap (#7) using 3068
atoms
average map value = 0.4144, steps = 96
shifted from previous position = 1.65
rotated from previous position = 17.1 degrees
atoms outside contour = 1606, contour level = 0.42499
Position of vsm_PDB-coot-0.pdb (#8) relative to P34_J1433.cmap (#7)
coordinates:
Matrix rotation and translation
-0.17401543 -0.74994712 -0.63819899 298.12375422
0.84629354 0.21747116 -0.48630601 42.23979286
0.50349366 -0.62472843 0.59683206 68.71960439
Axis -0.07035855 -0.58030948 0.81135109
Axis point 127.27727137 199.24167051 0.00000000
Rotation angle (degrees) 100.36137848
Shift along axis 10.26801754
> save D:/183/183-map/183-0708-PDB/vsm_resample.pdb models #8 relModel #7
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> surface dust #1 size 9.32
> surface dust #5 size 9.32
> surface dust #6 size 9.32
> surface dust #7 size 9.32
> hide #!1 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> select subtract #8
Nothing selected
> hide #!4 models
> hide #!3 models
> select ::name="ACH"
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel cyan
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:25-478
3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected
> color (#!2 & sel) dark gray
> hide sel atoms
> select #2/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #ff00ffff
> color sel #ff39ffff
> color sel #c02effff
> color sel #ffffffff
> color sel #ff00ffff
> color sel #dd35ffff
> color sel #b73cffff
> color sel #ffffffff
> color sel #ff00ffff
> color sel #ce39ffff
> color sel #b633e2ff
> color sel #a62eceff
> color sel #ce39ffff
> color sel #a62eceff
> select #2/A:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:396
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:396
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:394-395
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:394-395
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff7fff
> color sel #a62eceff
> select #2/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #a62eceff
> show #!3 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:25-26
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B
3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected
> color (#!3 & sel) dark gray
> select #3/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #ffffffff
> color sel #6449ffff
> color sel #7a46ffff
> color sel #8b3dffff
> color sel #a639ffff
> color sel #9c22ffff
> color sel #8018ffff
> color sel #790bffff
> color sel #8331ffff
> color sel #9b54ffff
> color sel #9c75ffff
> color sel #ffffffff
> color sel #6449ffff
> color sel #4520ffff
> color sel #430affff
> color sel #4208ffff
> color sel #a66affff
> color sel #896cffff
> color sel #6f71ffff
> color sel #aaff00ff
> color sel #6f71ffff
> select #3/B:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B:398-399
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #6f71ffff
> select #3/B:428-429
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/B:428-429
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/B:428-429
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/B:428-429
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/B:426
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:426-427
14 atoms, 13 bonds, 2 residues, 1 model selected
> select
> #3/B:28-60,122-147,152-171,176-203,207-236,244-263,268-273,282-287,289-308,312-319,324-328,333-351,356-376,380-411,418-445,448-460,463-468
2385 atoms, 2425 bonds, 321 residues, 1 model selected
> select #3/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #6f71ffff
> hide #!3 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A
3037 atoms, 3113 bonds, 1 pseudobond, 404 residues, 2 models selected
> color (#!4 & sel) dark gray
> select #4/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #c8bb2dff
> color sel #b6a829ff
> color sel #aaff00ff
> color sel #b6a829ff
> select #4/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #b6a829ff
> select #4/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #b6a829ff
> hide #!4 models
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:25-478
3049 atoms, 3125 bonds, 1 pseudobond, 405 residues, 2 models selected
> color (#!8 & sel) dark gray
> hide sel atoms
> select #8/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #5ba33bff
> select #8/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #5ba33bff
> select #8/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #aaff00ff
> color sel #5ba33bff
> hide #!8 models
> cartoon style width 0.7
> transparency 60 cartoons
> show #!2 models
> show #!3 models
> show #!4 models
> show #!8 models
> ui tool show "Side View"
> hide #!8 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!3 models
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 5.59
> volume splitbyzone #1
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 0 as #9.1, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 1 as #9.2, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 2 as #9.3, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 3 as #9.4, grid size
256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32
> hide #!9 models
> hide #!9.1 models
> hide #!9.2 models
> show #!9 models
> hide #!9.4 models
> volume #9.3 style mesh
> volume #9.3 level 0.5616
> transparency #2#9.3#!9 50
> transparency #2#9.3#!9 80
> transparency #2#9.3#!9 20
> select ::name="ACH"
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel byhetero
> color #9.3 #0000ffcc models
> color #9.3 #ffffffcc models
> color #9.3 blue models
> color #9.3 #6e61ffff models
> color #9.3 #868cffff models
> color #9.3 #a4b0ffff models
> color #9.3 #c1c7ffff models
> color #9.3 #a1aaffff models
> color #9.3 white models
> color #9.3 #5500ffff models
> color #9.3 #777effff models
> color #9.3 #8e8effff models
> color #9.3 black models
> color #9.3 #5153c8ff models
> color #9.3 #858fc8ff models
> color #9.3 #cce4f7ff models
> color #9.3 #ffaaffff models
> color #9.3 white models
> color #9.3 #aaaaffff models
> color #9.3 #4cc8a9ff models
> color #9.3 #4e5ec8ff models
> volume #9.3 style surface
> volume #9.3 style mesh
> hide #!9.3 models
> show #!9.3 models
> hide #!9.3 models
> show #!9.3 models
> hide #!9.3 models
> show #!3 models
> show #!9.3 models
> hide #!9.3 models
> hide #!3 models
> show #!9.3 models
> hide #!9.3 models
> ui mousemode right distance
> distance #2/A:428@OH #2/A:398@OD1
Distance between ACh.pdb #2/A TYR 428 OH and ASP 398 OD1: 2.654Å
> hide #10.1 models
> show #!9.3 models
> hide #!9.3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:476-478
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #2/A:25-478
3044 atoms, 3120 bonds, 2 pseudobonds, 404 residues, 3 models selected
> color (#!2 & sel) byhetero
> select #2/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!9.3 models
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> save D:/183/Fig-12/ach-d425-soft-1.png width 2000 height 2000 supersample 4
> transparentBackground true
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> lighting full
> lighting shadows false
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save D:/183/Fig-12/ach-d425-soft-1.png width 2000 height 2000 supersample 4
> transparentBackground true
> transparency sel 0
> transparency sel 100
> transparency sel 0
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> lighting full
> volume #9.3 style surface
> transparency sel 60
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #9.3 style mesh
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> save D:/183/Fig-12/1.png width 2000 height 2000 supersample 4
> transparentBackground true
> lighting full
> lighting shadows false
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> volume #9.3 color #ff55ff
> volume #9.3 color #55aaff
> volume #9.3 color blue
> lighting full
> lighting shadows false
> save D:/183/Fig-12/ChimeraX/398-ach.png width 2000 height 2000 supersample 4
> transparentBackground true
> hide #!10 models
> hide #!9.3 models
> close #10
> show #!3 models
> show #!5 models
> hide #!2 models
> show #!2 models
> color zone #5 near #3 distance 5.59
> volume splitbyzone #5
Opened P34_J608_004.cmap 0 as #10.1, grid size 256,256,256, pixel 0.932, shown
at level 0.506, step 1, values float32
Opened P34_J608_004.cmap 1 as #10.2, grid size 256,256,256, pixel 0.932, shown
at level 0.506, step 1, values float32
Opened P34_J608_004.cmap 2 as #10.3, grid size 256,256,256, pixel 0.932, shown
at level 0.506, step 1, values float32
> volume #10.3 style mesh
> hide #!2 models
> volume #10.3 level 0.362
> color #3#10.3#!9-10 byhetero
> save D:/183/Fig-12/ChimeraX/398-apo.png width 2000 height 2000 supersample 4
> transparentBackground true
> hide #!3 models
> show #!4 models
> show #!6 models
> color zone #6 near #4 distance 5.59
> volume splitbyzone #6
Opened P49_J393_003.cmap 0 as #11.1, grid size 256,256,256, pixel 0.932, shown
at level 0.411, step 1, values float32
Opened P49_J393_003.cmap 1 as #11.2, grid size 256,256,256, pixel 0.932, shown
at level 0.411, step 1, values float32
Opened P49_J393_003.cmap 2 as #11.3, grid size 256,256,256, pixel 0.932, shown
at level 0.411, step 1, values float32
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> hide #!11.1 models
> hide #!11.2 models
> volume #11.3 level 0.2013
> volume #11.3 style mesh
> color #4#11.3#!11 byhetero
> save D:/183/Fig-12/ChimeraX/398-5.5.png width 2000 height 2000 supersample 4
> transparentBackground true
> hide #!11 models
> hide #!11.3 models
> hide #!4 models
> show #!8 models
> show #!7 models
> color zone #7 near #8 distance 5.59
> hide #!8 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!11.3 models
> show #!4 models
> color #11.3 #4e5ec8ff models
> save D:/183/Fig-12/ChimeraX/398-5.5.png width 2000 height 2000 supersample 4
> transparentBackground true
> hide #!11 models
> hide #!11.3 models
> hide #!4 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!10.1 models
> hide #!10.1 models
> show #!10.3 models
> hide #!10.3 models
> hide #!10 models
> hide #7.1 models
> show #7.1 models
> color zone #7 near #8 distance 5.59
> volume splitbyzone #7
Opened P34_J1433.cmap 0 as #12.1, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 1 as #12.2, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 2 as #12.3, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 3 as #12.4, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 4 as #12.5, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 5 as #12.6, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
> hide #!12.1 models
> hide #!12.2 models
> hide #!12.5 models
> hide #!12.6 models
> select ::name="VSM"
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel yellow
> color zone #7 near #8 distance 5.59
> volume splitbyzone #7
Opened P34_J1433.cmap 0 as #13.1, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 1 as #13.2, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 2 as #13.3, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
Opened P34_J1433.cmap 3 as #13.4, grid size 256,256,256, pixel 0.932, shown at
level 0.425, step 1, values float32
> hide #!13.1 models
> hide #!13.2 models
> hide #!12.4 models
> hide #!12.3 models
> volume #13.3 level 0.1573
> volume #13.4
> volume #13.3 style mesh
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel byelement
> ui mousemode right select
> select #8/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #8/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #8/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:130-131
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> volume #13.3 color #4e5ec8
> select #8/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> save D:/183/Fig-12/ChimeraX/398-VSM.png width 2000 height 2000 supersample 4
> transparentBackground true
> ui mousemode right distance
> distance #8/A:428@OH #8/A:131@NZ
Distance between vsm_PDB-coot-0.pdb #8/A TYR 428 OH and LYS 131 NZ: 2.877Å
> hide #14.1 models
> save D:/183/Fig-12/ChimeraX/398-VSM.png width 2000 height 2000 supersample 4
> transparentBackground true
> save D:/183/Fig-12/ChimeraX/D398.cxs includeMaps true
——— End of log from Wed Dec 11 15:01:23 2024 ———
opened ChimeraX session
> hide #!13.3 models
> show #!13.3 models
> hide #!13.3 models
> show #!13.3 models
> show #!13.4 models
> hide #!13.4 models
> show #!13.2 models
> hide #!13.2 models
> show #!13.2 models
> hide #!13.2 models
> show #!13.2 models
> hide #!13.2 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> ui tool show Distances
Exactly two atoms must be selected!
> ui mousemode right select
> select clear
> ui mousemode right translate
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Hide Dust"
> surface dust #13.3 size 5.59
> surface dust #13.3 size 6.06
> surface dust #13.3 size 1.51
> ui tool show Distances
> distance style radius 0.2
> distance style radius 0.15
> hide #!13.3 models
> show #!13.3 models
> hide #!13.3 models
> show #!13.3 models
> hide #!13.3 models
> show #!13.3 models
> hide #!13.3 models
> show #!13.3 models
> show #!13.1 models
> hide #!13 models
> hide #!13.1 models
> show #!13.2 models
> hide #!13.2 models
> hide #!13.3 models
> show #!13.3 models
> hide #!13 models
> show #!12.5 models
> hide #!12.5 models
> show #!12.6 models
> hide #!12.6 models
> show #!12.4 models
> hide #!12.4 models
> show #!12.3 models
> hide #!12.3 models
> show #!12.3 models
> hide #!12.3 models
> show #!12.2 models
> hide #!12.2 models
> show #!12.1 models
> hide #!12.1 models
> hide #!12 models
> show #!12 models
> close #12
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> rename #13 "VSM_P34_J1433.cmap split"
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!11.3 models
> hide #!11.3 models
> show #!11.3 models
> volume #11.3 level 0.1415
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!8 models
> show #!4 models
> volume #11.3 level 0.1938
> surface dust #11.3 size 5.59
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> rename #11 "PRO_P49_J393_003.cmap split"
> hide #!11 models
> show #!10.3 models
> rename #10 "APO_P34_J608_004.cmap split"
> hide #!4 models
> show #!3 models
> color #10.3 #5869cfff models
> hide #!10.3 models
> show #!10.3 models
> hide #!10.3 models
> show #!10.3 models
> hide #!10.3 models
> show #!10.3 models
> hide #!10.3 models
> show #!10.3 models
> hide #!10.3 models
> show #!10.3 models
> surface dust #10.3 size 5.59
> volume #10.3 level 0.2697
> hide #!10 models
> show #!9 models
> show #!9.3 models
> color #9.3 #6374d5ff models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> rename #9 "ACh——cryosparc_P34_J1741_003_volume_map_sharp.mrc split"
> rename #9 "ACh_cryosparc_P34_J1741_003_volume_map_sharp.mrc split"
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> show #!3 models
> show #!4 models
> ui mousemode right select
> hide #!4 models
> hide #!3 models
> open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT-
> zw/183_structure/VAChT-ACh/VAChT-ACh.pdb
Chain information for VAChT-ACh.pdb #12
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> select add #12
3054 atoms, 3129 bonds, 1 pseudobond, 405 residues, 2 models selected
> select subtract #12
Nothing selected
> hide #!2 models
> select #12/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> select add #12
3054 atoms, 3129 bonds, 1 pseudobond, 405 residues, 2 models selected
> select subtract #12
Nothing selected
> hide #!12 models
> show #!12 models
> close #12
> open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT-
> zw/183_structure/VAChT-apo/VAChT-apo.pdb
Chain information for VAChT-apo.pdb #12
---
Chain | Description
B | No description available
Computing secondary structure
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #12
3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected
> show sel atoms
> select subtract #12
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #3
> select add #12
3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected
> hide sel atoms
> select subtract #12
Nothing selected
> hide #!2 models
> select #12/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/B:425
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #12/B:425
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> show #!2 models
> hide #!2 models
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!2 models
> select #12/B:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!2 models
> hide #!12 models
> show #!12 models
> show #!4 models
> hide #!4 models
> color #12 #a99e2aff
> color #12 #a9a92aff
> color #12 darkgrey
> show #!2 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!2 models
> hide #2.1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #12
3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> undo
> hide #!12 models
> show #!2 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> color #12 #a9a9a981
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> color #12 #d8d8d8ff
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> color #12 #d8d8d895
> color #12 #d8d8d858
> color #12 #d8d8d868
> color #12 #d8d8d867
> color #12 #d8d8d866
> select clear
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> cartoon style width 1
> hide #!2 models
> show #!2 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> color #12 #d8d8d8fa
> color #12 #d8d8d8ff
> color #12 #d8d8d8dc
> color #12 #d8d8d8ff
> color #12 #d8d8d8ec
> color #12 #d8d8d8cb
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #12 #ebebebff
> color #12 #ebebebc5
> color #12 #ebebebcd
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!2 models
> show #!2 models
> show #!12 models
> color #12 #b2b2b2ff
> color #12 #b2b2b278
> color #12 #b2b2b280
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!2 models
> show #!12 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #b2b2b280
> color sel #70b2b280
> color sel #7090b280
> color sel #7090dd80
> color sel #7090dd81
> color sel #7090dd86
> color sel #7090dd8f
> color sel #7090dd99
> color sel #7090dd9a
> color sel #7090dda7
> color sel #7090ddb2
> color sel #7090ddba
> color sel #7090ddc2
> color sel #7090ddc7
> color sel #7090ddcd
> color sel #7090ddd5
> color sel #7090dddc
> color sel #7090ddde
> color sel #7090dde1
> color sel #7090dde2
> color sel #7090dde5
> color sel #7090dde7
> color sel #7090dded
> color sel #7090ddf2
> color sel #7090ddf5
> color sel #7090ddf7
> color sel #7090ddf8
> color sel #7090ddfa
> color sel #7090ddfb
> color sel #7090ddfc
> color sel #7090ddfd
> color sel #7090ddfe
> color sel #7090ddff
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #7090ddff
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #7090ddff
> color sel byhetero
> select clear
> show #!10 models
> hide #!10 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> select #12/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #12/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #12/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #12/B:428@CZ
1 atom, 1 residue, 1 model selected
> select clear
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select #12/B:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> hide #!12 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!12 models
> transparency 50 cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!12 models
> show #!4 models
> hide #!4 models
> show #!4 models
> open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT-
> zw/183_structure/VAChT-protonated/VAChT-protonated.pdb
Chain information for VAChT-protonated.pdb #3
---
Chain | Description
A | No description available
> hide #!4 models
> show #!4 models
> select add #3
3037 atoms, 3112 bonds, 1 pseudobond, 404 residues, 2 models selected
> show sel atoms
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide sel atoms
> select subtract #3
Nothing selected
> hide #!4 models
> select #3/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> select #3/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> select #3/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> select add #3/A:428
20 atoms, 19 bonds, 2 residues, 1 model selected
> show #!4 models
> hide #!4 models
> select add #3/A:131
29 atoms, 27 bonds, 3 residues, 1 model selected
> color #3 #b2b2b2ff
> color #3 #b2b2b280
> show sel atoms
> color sel #f3c27880
> color sel #f3c27881
> color sel #f3c27883
> color sel #f3c27885
> color sel #f3c27887
> color sel #f3c27890
> color sel #f3c2789a
> color sel #f3c278a2
> color sel #f3c278af
> color sel #f3c278be
> color sel #f3c278ca
> color sel #f3c278cf
> color sel #f3c278d4
> color sel #f3c278d9
> color sel #f3c278e4
> color sel #f3c278e8
> color sel #f3c278ee
> color sel #f3c278f4
> color sel #f3c278fc
> color sel #f3c278ff
> color sel byhetero
> select clear
> transparency 50 cartoons
> cartoon style width 1
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.1902
> ui tool show "Color Zone"
> color zone #6 near #3 distance 5.44
> color zone #6 near #3 distance 38.72
> color zone #6 near #3 distance 14.77
> color zone #6 near #3 distance 27.91
> color zone #6 near #3 distance 30.01
> color zone #6 near #3 distance 87.72
> hide #!6 models
> select #3/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/A:428
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #3/A:131
29 atoms, 27 bonds, 3 residues, 1 model selected
> color sel #f3c278ff
> show #!6 models
> color zone #6 near #3 distance 87.72
> ui tool show "Side View"
> color zone #6 near #3 distance 96.1
> color zone #6 near #3 distance 175.03
> color zone #6 near #3 distance 195.22
> color zone #6 near #3 distance 411.35
> color zone #6 near #3 distance 396.57
> color zone #6 near #3 distance 932
> volume splitbyzone #6
Opened P49_J393_003.cmap 0 as #15.1, grid size 256,256,256, pixel 0.932, shown
at level 0.19, step 1, values float32
Opened P49_J393_003.cmap 1 as #15.2, grid size 256,256,256, pixel 0.932, shown
at level 0.19, step 1, values float32
Opened P49_J393_003.cmap 2 as #15.3, grid size 256,256,256, pixel 0.932, shown
at level 0.19, step 1, values float32
> hide #!15.1 models
> hide #!15.2 models
> volume #15.3 style mesh
> select clear
> volume #15.3 level 0.1341
> volume #15.3 color #5869cf
> volume #15.3 level 0.2089
> select #3/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/A:428
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #3/A:131
29 atoms, 27 bonds, 3 residues, 1 model selected
> color sel byhetero
> select clear
> transparency 50 cartoons
> select clear
> surface dust #15.2 size 5.59
> surface dust #15.2 size 5.86
> surface dust #15.2 size 6.37
> surface dust #15.3 size 5.59
> transparency 80 mesh
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 80 surfaces
> transparency 90 surfaces
> transparency 10 surfaces
> transparency 30 surfaces
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #4
> show #!8 models
> hide #!15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT-
> zw/183_structure/VAChT-VSM/VAChT-VSM.pdb
Chain information for VAChT-VSM.pdb #4
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #4/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #4/A:131
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #!13 models
> volume #13.3 level 0.1776
> volume #13.3 level 0.1857
> hide #!13 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select clear
> select add #4
3070 atoms, 3148 bonds, 1 pseudobond, 406 residues, 2 models selected
> hide sel atoms
> select ::name="VSM"
38 atoms, 42 bonds, 2 residues, 2 models selected
> select clear
> select ::name="VSM"
38 atoms, 42 bonds, 2 residues, 2 models selected
> show sel & #!4 atoms
> color (#!4 & sel) yellow
> color (#!4 & sel) byhetero
> select clear
> color #4 #bbbbbbff
> color #4 #bbbbbb80
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel #bbbbbb80
> color sel #bbbbbb86
> color sel #bbbbbba6
> color sel #bbbbbbb0
> color sel #bbbbbbb7
> color sel #bbbbbbc0
> color sel #bbbbbbca
> color sel #bbbbbbcb
> color sel #bbbbbbd6
> color sel #bbbbbbe1
> color sel #bbbbbbf0
> color sel #bbbbbbff
> color sel #fffb00ff
> color sel byhetero
> select clear
> cartoon style width 1
> show #!8 models
> hide #!8 models
> select #4/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!8 models
> hide #!8 models
> select add #4/A:428
20 atoms, 19 bonds, 2 residues, 1 model selected
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #4/A:131
29 atoms, 27 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel #fffb00ff
> color sel #68d587ff
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> color sel byhetero
> select clear
> transparency 50 cartoons
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!8 models
> show #!8 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!15 models
> hide #!15 models
> rename #15 "PROP49_J393_003.cmap split"
> rename #15 "PRO_P49_J393_003.cmap split"
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!13 models
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/250515_D398.cxs
> includeMaps true
> ui tool show "Side View"
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting full
> hide #!8 models
> hide #!13 models
> show #!15 models
> show #!3 models
> hide #!3 models
> hide #!15 models
> show #!12 models
> show #!10 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!4 models
> hide #!12 models
> hide #!10 models
> hide #!4 models
> show #!2 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> surface dust #9.3 size 5.59
> hide #!9 models
> hide #!2 models
> show #!3 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!3 models
> show #!13 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!13 models
> show #!10 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!10 models
> show #!15 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!15 models
> hide #!3 models
> show #!12 models
> show #!10 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> ui tool show Distances
> select #12/B:428@OH
1 atom, 1 residue, 1 model selected
> select add #12/B:398@OD1
2 atoms, 2 residues, 1 model selected
> distance #12/B:428@OH #12/B:398@OD1
Distance between VAChT-apo.pdb #12/B TYR 428 OH and ASP 398 OD1: 2.655Å
> distance #12/B:428@OH #12/B:398@OD1
Distance already exists; modify distance properties with 'distance style'
> distance style symbol false
> distance style symbol true
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> distance style symbol false
> distance style symbol true
> distance style symbol false
> distance style symbol true
> distance style symbol false
> distance style symbol true
> distance style symbol false
> distance style dashes 8
> distance style decimalPlaces 2
> distance style decimalPlaces 3
> distance style dashes 9
> distance style radius 0.1
> distance style symbol true
> distance style decimalPlaces 2
> distance style dashes 10
> distance style dashes 9
> distance style dashes 8
> distance style dashes 7
> distance style radius 0.15
> stick width 1
Unknown command: stick width 1
> style stick thick 1
Expected a keyword
> style stick ringFill thick 1
Expected a keyword
> style stick ringFill thick 2
Expected a keyword
> style stick ringFill thick
Changed 15273 atom styles, 2025 residue ring styles
> style stick ringFill thick dashes 2
Changed 15273 atom styles, 6 pseudobond dashes, 2025 residue ring styles
> undo
> size stickRadius 2
Changed 15655 bond radii
> size stickRadius 1
Changed 15655 bond radii
> size stickRadius 0.5
Changed 15655 bond radii
> size stickRadius 0.3
Changed 15655 bond radii
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/250515_D398.cxs
> includeMaps true
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398APO.png
> width 1341 height 1019 supersample 3 transparentBackground true
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398APO.png
> width 1000 height 1000 supersample 3 transparentBackground true
> hide #!14 models
> hide #!12 models
> hide #!10 models
> show #!14 models
> hide #!14 models
> show #!4 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> select #4/A:131@NZ
1 atom, 1 residue, 1 model selected
> select add #4/A:428@OH
2 atoms, 2 residues, 1 model selected
> distance #4/A:131@NZ #4/A:428@OH
Distance between VAChT-VSM.pdb #4/A LYS 131 NZ and TYR 428 OH: 2.88Å
> select clear
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png
> width 1000 height 1000 supersample 3 transparentBackground true
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png
> width 500 height 500 supersample 3 transparentBackground true
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png
> width 500 height 500 supersample 1 transparentBackground true
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png
> width 500 height 500 supersample 3 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save
> /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM_nomiaobian.png
> width 1000 height 1000 supersample 3 transparentBackground true
> volume #13.3 style surface
> volume #13.3 style mesh
> volume #13.3 style surface
> volume #13.3 color #4e5ec81f
> volume #13.3 color #4e5ec800
> volume #13.3 color #4e5ec832
> select #4/A:428
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #4e5ec833
> color sel #4e5ec83c
> color sel #4e5ec8b5
> color sel #4e5ec8b8
> color sel #4e5ec8b9
> color sel #4e5ec8c0
> color sel #4e5ec8c3
> color sel #4e5ec8ca
> color sel #4e5ec8cc
> color sel #4e5ec8ce
> color sel #4e5ec8cf
> color sel #4e5ec8d0
> color sel #4e5ec8d1
> color sel #4e5ec8d2
> color sel #4e5ec8d3
> color sel #4e5ec8d4
> color sel #4e5ec8d5
> color sel #4e5ec8d6
> color sel #4e5ec8d7
> color sel #4e5ec8d8
> color sel #4e5ec8d9
> color sel #4e5ec8e2
> color sel #4e5ec8f0
> color sel #4e5ec8f7
> color sel #4e5ec8fa
> color sel #4e5ec8fb
> color sel #4e5ec8ff
> undo
> color sel #68d587ff
> color sel byhetero
> select clear
> color #4 #ebebebff
> color #4 #d6d6d6ff
> undo
> select #13.3
2 models selected
> select clear
> select #4/A:131@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> color sel #d6d6d6ff
> color sel #68d587ff
> color sel byhetero
> select clear
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
===== 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
> open /Users/feiwenwei/Downloads/emd_38652.map
Opened emd_38652.map as #1, grid size 256,256,256, pixel 0.85, shown at level
0.414, step 1, values float32
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: MacBookPro18,3
Model Number: MKGR3CH/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 3天5小时52分钟
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
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
DELL U2719D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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