![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 weeks ago
Closed 7 weeks ago
#18812 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6-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 0x000000020abb20c0 (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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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, lxml._elementpath, lxml.etree, chimerax.graphics._graphics, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 60)
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"procRole" : "Foreground",
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"modelCode" : "Mac14,2",
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"incident" : "C50138D7-06C3-4812-9247-B4BE28A1A1F2",
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"cpuType" : "ARM-64",
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"procLaunch" : "2025-09-16 16:33:32.3868 +0800",
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"procExitAbsTime" : 51183492855777,
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"crashReporterKey" : "72006326-E93A-79ED-CE4E-652FF4F2A5CE",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["countryBillingIneligible","countryLocationIneligible","regionIneligible"]},
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "85235F47-BC84-4CDC-AC02-17DF3D83FD33",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x00000e328552f708","rawCodes":[1,15610147960584],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000e328552f708"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":14301},
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=7.6G written=410.0M(5%) resident=4770K(0%) swapped_out=405.3M(5%) unallocated=7.2G(95%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 2528K 56 \nColorSync 704K 38 \nCoreAnimation 4384K 165 \nCoreGraphics 160K 10 \nCoreImage 96K 3 \nCoreUI image data 2192K 19 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 6.6G 171 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 191.2M 36 \nVM_ALLOCATE 742.0M 279 \n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 34.3M 1090 \n__DATA_CONST 37.0M 1107 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 648.9M 158 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1126 \n__TEXT (graphics) 496K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 3616K 31 \nmapped file 635.7M 111 \npage table in kernel 4770K 1 \nshared memory 3152K 22 \n=========== ======= ======= \nTOTAL 10.4G 6480 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "0d8251ec21904051cfb07435e512bc7a0d74dd61",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "648cada15dbc71671bb3aa1b",
"factorPackIds" : {
"SIRI_EXPERIENCE_CAM" : "65a81173096f6a1f1ba46525"
},
"deploymentId" : 240000116
},
{
"rolloutId" : "66d35d7fe4d6bf7664f40ddf",
"factorPackIds" : {
"BLACKPEARL_SPARROW" : "67c7824a1baae429bb41b897"
},
"deploymentId" : 240000067
}
],
"experiments" : [
]
}
}
===== 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/chenxi/Desktop/RH-figure/map align.cxs"
Opened J1551_009_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 1.1,
shown at level 0.287, step 1, values float32
Opened J1594_005_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 1.1,
shown at level 0.226, step 1, values float32
Opened J75_011_volume_map.mrc as #4, grid size 384,384,384, pixel 1.1, shown
at level 0.297, step 1, values float32
Opened 切整个blade-postprocess_masked_job217_blade.mrc z flip as #8, grid size
192,192,192, pixel 2.2, shown at level 0.0347, step 1, values float32
Opened 5z10_low5.mrc as #9, grid size 280,280,280, pixel 1.32, shown at level
0.0411, step 1, values float32
Opened 8IXO-35800_low8.mrc as #11, grid size 368,368,368, pixel 1.1, shown at
level 6.84, step 2, values float32
Opened RH_patfla_J76_006_volume_map_sharp_low8.mrc as #12, grid size
196,196,196, pixel 2.2, shown at level 0.869, step 1, values float32
Opened RH-detergent-composite_map-j126_low8.mrc z flip as #14, grid size
400,400,400, pixel 1.1, shown at level 9.33, step 1, values float32
Opened 8IXO-35800_low8.mrc z flip as #15, grid size 368,368,368, pixel 1.1,
shown at level 7.41, step 1, values float32
Opened 7wlu.map as #16, grid size 180,180,180, pixel 2.2, shown at level
0.0204, step 1, values float32
Opened 7wlu_low8.mrc as #17, grid size 180,180,180, pixel 2.2, shown at level
0.0205, step 1, values float32
Log from Thu Aug 21 16:31:39 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/chenxi/Desktop/RH-figure/map align.cxs"
Opened J1551_009_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 1.1,
shown at level 0.287, step 1, values float32
Opened J1594_005_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 1.1,
shown at level 0.226, step 1, values float32
Opened J75_011_volume_map.mrc as #4, grid size 384,384,384, pixel 1.1, shown
at level 0.297, step 1, values float32
Opened 切整个blade-postprocess_masked_job217_blade.mrc z flip as #8, grid size
192,192,192, pixel 2.2, shown at level 0.0347, step 1, values float32
Opened 5z10_low5.mrc as #9, grid size 280,280,280, pixel 1.32, shown at level
0.0411, step 1, values float32
Opened 8IXO-35800_low8.mrc as #11, grid size 368,368,368, pixel 1.1, shown at
level 6.84, step 2, values float32
Opened RH_patfla_J76_006_volume_map_sharp_low8.mrc as #12, grid size
196,196,196, pixel 2.2, shown at level 0.869, step 1, values float32
Opened RH-detergent-composite_map-j126_low8.mrc z flip as #14, grid size
400,400,400, pixel 1.1, shown at level 9.33, step 1, values float32
Opened 8IXO-35800_low8.mrc z flip as #15, grid size 368,368,368, pixel 1.1,
shown at level 7.41, step 1, values float32
Opened 7wlu.map as #16, grid size 180,180,180, pixel 2.2, shown at level
0.0204, step 1, values float32
Opened 7wlu_low8.mrc as #17, grid size 180,180,180, pixel 2.2, shown at level
0.0205, step 1, values float32
Log from Wed Aug 20 15:25:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/chenxi/Desktop/map-align.cxs
Opened J1551_009_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 1.1,
shown at level 0.287, step 1, values float32
Opened J1594_005_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 1.1,
shown at level 0.226, step 1, values float32
Opened 8IXO.map as #3, grid size 368,368,368, pixel 1.1, shown at level 10.9,
step 1, values float32
Opened 5z10.map as #6, grid size 280,280,280, pixel 1.32, shown at level
0.045, step 1, values float32
Opened RH_patfla_J76_006_volume_map_sharp.mrc as #10, grid size 196,196,196,
pixel 2.2, shown at level 0.894, step 1, values float32
Opened J75_011_volume_map.mrc as #4, grid size 384,384,384, pixel 1.1, shown
at level 0.297, step 1, values float32
Opened RH-detergent-composite_map-j126.ccp4 as #5, grid size 400,400,400,
pixel 1.1, shown at level 5.1, step 2, values float32
Opened 切整个blade-postprocess_masked_job217_blade.mrc as #7, grid size
192,192,192, pixel 2.2, shown at level 0.0331, step 1, values float32
Opened 切整个blade-postprocess_masked_job217_blade.mrc z flip as #8, grid size
192,192,192, pixel 2.2, shown at level 0.0347, step 1, values float32
Opened 5z10_low5.mrc as #9, grid size 280,280,280, pixel 1.32, shown at level
0.0411, step 1, values float32
Opened 8IXO-35800_low8.mrc as #11, grid size 368,368,368, pixel 1.1, shown at
level 6.84, step 2, values float32
Opened RH_patfla_J76_006_volume_map_sharp_low8.mrc as #12, grid size
196,196,196, pixel 2.2, shown at level 0.869, step 1, values float32
Opened RH-detergent-composite_map-j126_low8.mrc as #13, grid size 400,400,400,
pixel 1.1, shown at level 5.47, step 1, values float32
Opened RH-detergent-composite_map-j126_low8.mrc z flip as #14, grid size
400,400,400, pixel 1.1, shown at level 9.33, step 1, values float32
Opened 8IXO-35800_low8.mrc z flip as #15, grid size 368,368,368, pixel 1.1,
shown at level 7.41, step 1, values float32
Opened 7wlu.map as #16, grid size 180,180,180, pixel 2.2, shown at level
0.0204, step 1, values float32
Opened 7wlu_low8.mrc as #17, grid size 180,180,180, pixel 2.2, shown at level
0.0205, step 1, values float32
Log from Wed Aug 20 01:50:05 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/chenxi/Desktop/map-align.cxs
Opened J1551_009_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 1.1,
shown at level 0.287, step 1, values float32
Opened J1594_005_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 1.1,
shown at level 0.226, step 1, values float32
Opened 8IXO.map as #3, grid size 368,368,368, pixel 1.1, shown at level 10.9,
step 1, values float32
Opened 5z10.map as #6, grid size 280,280,280, pixel 1.32, shown at level
0.045, step 1, values float32
Opened RH_patfla_J76_006_volume_map_sharp.mrc as #10, grid size 196,196,196,
pixel 2.2, shown at level 0.894, step 1, values float32
Opened J75_011_volume_map.mrc as #4, grid size 384,384,384, pixel 1.1, shown
at level 0.297, step 1, values float32
Opened RH-detergent-composite_map-j126.ccp4 as #5, grid size 400,400,400,
pixel 1.1, shown at level 5.1, step 2, values float32
Opened 切整个blade-postprocess_masked_job217_blade.mrc as #7, grid size
192,192,192, pixel 2.2, shown at level 0.0331, step 1, values float32
Opened 切整个blade-postprocess_masked_job217_blade.mrc z flip as #8, grid size
192,192,192, pixel 2.2, shown at level 0.0347, step 1, values float32
Opened 5z10_low5.mrc as #9, grid size 280,280,280, pixel 1.32, shown at level
0.0411, step 1, values float32
Opened 8IXO-35800_low8.mrc as #11, grid size 368,368,368, pixel 1.1, shown at
level 6.84, step 2, values float32
Opened RH_patfla_J76_006_volume_map_sharp_low8.mrc as #12, grid size
196,196,196, pixel 2.2, shown at level 0.869, step 1, values float32
Opened RH-detergent-composite_map-j126_low8.mrc as #13, grid size 400,400,400,
pixel 1.1, shown at level 5.47, step 1, values float32
Opened RH-detergent-composite_map-j126_low8.mrc z flip as #14, grid size
400,400,400, pixel 1.1, shown at level 9.33, step 1, values float32
Opened 8IXO-35800_low8.mrc z flip as #15, grid size 368,368,368, pixel 1.1,
shown at level 7.41, step 1, values float32
Opened 7wlu.map as #16, grid size 180,180,180, pixel 2.2, shown at level
0.0204, step 1, values float32
Opened 7wlu_low8.mrc as #17, grid size 180,180,180, pixel 2.2, shown at level
0.0205, step 1, values float32
Log from Tue Aug 19 20:49:45 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sun Aug 17 02:57:48 2025 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/chenxi/Desktop/0808rhlip_all/rhlipc0808/J1551_009_volume_map_sharp.mrc
Opened J1551_009_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 1.1,
shown at level 0.181, step 2, values float32
> open
> /Users/chenxi/Desktop/0808rhlip_all/rhlipf0808/J1594_005_volume_map_sharp.mrc
Opened J1594_005_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 1.1,
shown at level 0.19, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> open /Users/chenxi/Desktop/PDB/8IXO.map
Opened 8IXO.map as #3, grid size 368,368,368, pixel 1.1, shown at level 6.59,
step 2, values float32
> select add #3
2 models selected
> hide #!2 models
> volume #1 level 0.2871
> volume #3 level 8.23
> volume #3 step 1
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,15.004,0,1,0,25.48,0,0,1,5.1296
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91248,-0.40269,-0.072244,138.01,0.40436,0.91455,0.009617,-42.841,0.062198,-0.037988,0.99734,1.004
> view matrix models
> #3,0.9179,-0.39641,-0.017668,123.82,0.39679,0.91736,0.031906,-46.627,0.0035601,-0.036298,0.99933,12.557
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.9179,-0.39641,-0.017668,125.02,0.39679,0.91736,0.031906,-51.75,0.0035601,-0.036298,0.99933,36.354
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.9715,-0.2359,-0.023377,79.413,0.23588,0.97178,-0.0035541,-22.327,0.023555,-0.0020613,0.99972,24.481
> fitmap #3 inMap #1
Fit map 8IXO.map in map J1551_009_volume_map_sharp.mrc using 266659 points
correlation = 0.6403, correlation about mean = 0.158, overlap = 5.069e+05
steps = 124, shift = 10.2, angle = 5.29 degrees
Position of 8IXO.map (#3) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.95077152 -0.30025962 -0.07666608 101.65888021
0.30298255 0.95262762 0.02649905 -39.34874348
0.06507763 -0.04842303 0.99670463 18.54034828
Axis -0.12003203 -0.22708641 0.96644921
Axis point 168.42480448 316.81329295 0.00000000
Rotation angle (degrees) 18.18535049
Shift along axis 14.65154857
> view matrix models
> #3,0.95109,-0.30721,-0.032384,93.673,0.3084,0.9503,0.042587,-43.411,0.017691,-0.050491,0.99857,28.583
> view matrix models
> #3,0.97863,-0.20548,-0.0080617,60.16,0.20562,0.97727,0.051654,-29.664,-0.0027354,-0.052207,0.99863,33.252
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97863,-0.20548,-0.0080617,61.034,0.20562,0.97727,0.051654,-31.143,-0.0027354,-0.052207,0.99863,42.887
> view matrix models
> #3,0.97863,-0.20548,-0.0080617,65.034,0.20562,0.97727,0.051654,-32.77,-0.0027354,-0.052207,0.99863,42.557
> fitmap #3 inMap #1
Fit map 8IXO.map in map J1551_009_volume_map_sharp.mrc using 266659 points
correlation = 0.633, correlation about mean = 0.3118, overlap = 5.535e+05
steps = 228, shift = 3.13, angle = 2.93 degrees
Position of 8IXO.map (#3) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.97586554 -0.21837214 -0.00021759 66.62038571
0.21837189 0.97586163 0.00279432 -22.39102091
-0.00039786 -0.00277439 0.99999607 34.01171792
Axis -0.01274948 0.00041274 0.99991864
Axis point 134.88752724 292.10501914 0.00000000
Rotation angle (degrees) 12.61447471
Shift along axis 33.15033408
> volume #3 level 10.85
> surface dust #3 size 11
> select subtract #3
Nothing selected
> hide #!3 models
> show #!2 models
> select add #2
2 models selected
> volume #2 level 0.3525
> view matrix models #2,1,0,0,-4.2303,0,1,0,7.5272,0,0,1,19.543
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.59359,-0.78937,-0.1567,578.37,-0.68854,0.59894,-0.40888,354.17,0.41661,-0.13481,-0.89903,406.96
> view matrix models
> #2,-0.63012,-0.74791,0.20874,490.28,-0.73169,0.48192,-0.48206,408.17,0.25994,-0.45649,-0.85091,504.78
> view matrix models
> #2,-0.87292,-0.47691,0.10282,509.33,-0.46547,0.75104,-0.46827,282.49,0.1461,-0.45662,-0.87758,537.26
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.87292,-0.47691,0.10282,478.11,-0.46547,0.75104,-0.46827,268.57,0.1461,-0.45662,-0.87758,533.44
> view matrix models
> #2,-0.87292,-0.47691,0.10282,476.45,-0.46547,0.75104,-0.46827,263.2,0.1461,-0.45662,-0.87758,523.26
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.84119,-0.52076,0.14567,468.98,-0.5294,0.73821,-0.41806,268.82,0.11017,-0.42878,-0.89667,529.69
> view matrix models
> #2,-0.88673,-0.45478,-0.083023,518.82,-0.43692,0.88312,-0.1709,155.73,0.15104,-0.11526,-0.98178,469.08
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.88673,-0.45478,-0.083023,525.29,-0.43692,0.88312,-0.1709,160.4,0.15104,-0.11526,-0.98178,467.31
> view matrix models
> #2,-0.88673,-0.45478,-0.083023,527.79,-0.43692,0.88312,-0.1709,162.45,0.15104,-0.11526,-0.98178,477.91
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.81302,-0.57978,-0.053415,532.37,-0.57783,0.81473,-0.048313,181.16,0.07153,-0.0084144,-0.9974,475.48
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.81302,-0.57978,-0.053415,531.27,-0.57783,0.81473,-0.048313,179.87,0.07153,-0.0084144,-0.9974,470.8
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.8438,-0.53472,-0.04552,526.17,-0.53269,0.84485,-0.049769,163,0.065069,-0.017747,-0.99772,474.49
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.8438,-0.53472,-0.04552,529.89,-0.53269,0.84485,-0.049769,164.62,0.065069,-0.017747,-0.99772,473.89
> view matrix models
> #2,-0.8438,-0.53472,-0.04552,531.31,-0.53269,0.84485,-0.049769,164.38,0.065069,-0.017747,-0.99772,476.99
> fitmap #2 inMap #1
Fit map J1594_005_volume_map_sharp.mrc in map J1551_009_volume_map_sharp.mrc
using 103469 points
correlation = 0.5221, correlation about mean = 0.1319, overlap = 8476
steps = 80, shift = 3.17, angle = 2.79 degrees
Position of J1594_005_volume_map_sharp.mrc (#2) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.86193748 -0.50600816 -0.03192991 526.36240693
-0.50574999 0.86252613 -0.01629771 144.41204529
0.03578716 0.00210095 -0.99935722 480.00494932
Axis 0.26219184 -0.96500876 0.00367902
Axis point 278.43511055 0.00000000 245.06267143
Rotation angle (degrees) 177.98929361
Shift along axis 0.41498455
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select subtract #2
Nothing selected
> show #!3 models
> show #!1 models
> hide #!2 models
> volume gaussian #1 sDev 2
Opened J1551_009_volume_map_sharp.mrc gaussian as #4, grid size 400,400,400,
pixel 1.1, shown at step 1, values float32
> volume #4 level 0.223
> volume gaussian #3 sDev 2
Opened 8IXO.map gaussian as #5, grid size 368,368,368, pixel 1.1, shown at
step 1, values float32
> volume #5 level 6.054
> volume #5 level 6.283
> show #!2 models
> volume #2 level 0.2258
> surface dust #2 size 11
> surface dust #4 size 11
> surface dust #5 size 11
> open /Users/chenxi/Desktop/PDB/5z10.map
Opened 5z10.map as #6, grid size 280,280,280, pixel 1.32, shown at level
0.0277, step 2, values float32
> hide #!2 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> select add #6
2 models selected
> ui tool show "Selection Inspector"
> view matrix models #6,1,0,0,38.714,0,1,0,31.066,0,0,1,-6.5143
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99898,0.011943,0.043591,27.652,-0.01293,0.99966,0.022436,28.989,-0.043308,-0.022977,0.9988,6.4275
> view matrix models
> #6,0.94186,-0.32329,0.091504,94.586,0.32149,0.94629,0.034251,-26.065,-0.097663,-0.0028422,0.99522,13.461
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.94186,-0.32329,0.091504,91.852,0.32149,0.94629,0.034251,-12.901,-0.097663,-0.0028422,0.99522,51.536
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9411,-0.31458,0.12394,83.653,0.31757,0.94822,-0.0046646,-4.5908,-0.11606,0.043751,0.99228,46.444
> view matrix models
> #6,0.93705,-0.32741,0.12139,87.465,0.33088,0.94363,-0.0089927,-5.3153,-0.1116,0.048592,0.99256,44.592
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.93705,-0.32741,0.12139,78.188,0.33088,0.94363,-0.0089927,-11.303,-0.1116,0.048592,0.99256,44.623
> volume #6 step 1
> volume #6 level 0.04866
> view matrix models
> #6,0.93705,-0.32741,0.12139,78.985,0.33088,0.94363,-0.0089927,-12.404,-0.1116,0.048592,0.99256,48.939
> view matrix models
> #6,0.93705,-0.32741,0.12139,73.55,0.33088,0.94363,-0.0089927,-13.064,-0.1116,0.048592,0.99256,50.354
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.92383,-0.36594,0.11238,85.482,0.36922,0.9293,-0.0091029,-17.314,-0.10111,0.049904,0.99362,47.93
> view matrix models
> #6,0.93524,-0.35054,0.04952,93.208,0.35313,0.93361,-0.06051,-4.6416,-0.025022,0.074079,0.99694,28.348
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.93524,-0.35054,0.04952,97.957,0.35313,0.93361,-0.06051,-5.8995,-0.025022,0.074079,0.99694,27.484
> fitmap #6 inMap #1
Fit map 5z10.map in map J1551_009_volume_map_sharp.mrc using 58039 points
correlation = 0.8522, correlation about mean = 0.5767, overlap = 1673
steps = 156, shift = 2.89, angle = 5.63 degrees
Position of 5z10.map (#6) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.91271256 -0.40860025 0.00127324 126.09641557
0.40860090 0.91271311 -0.00029264 -24.50141373
-0.00104253 0.00078734 0.99999915 35.92825056
Axis 0.00132156 0.00283377 0.99999511
Axis point 120.61056014 282.72380987 0.00000000
Rotation angle (degrees) 24.11708079
Shift along axis 36.02528735
> select subtract #6
Nothing selected
> volume gaussian #6 sDev 2
Opened 5z10.map gaussian as #7, grid size 280,280,280, pixel 1.32, shown at
step 1, values float32
> show #!4 models
> show #!5 models
> show #!2 models
> hide #!1 models
> color #7 #e6ffb2ff models
> color #7 #e66db2ff models
> color #7 #e66d50ff models
> color #7 #826d50ff models
> color #7 #8a6d50ff models
> color #7 #8ab050ff models
> color #7 #8ab07cff models
> color #2 #e6ffb2ff models
> color #2 #e66db2ff models
> color #2 #e66d50ff models
> color #4 #b2b270ff models
> color #4 #b27270ff models
> color #4 #297270ff models
> color #5 #e7b2ffff models
> color #5 #e7c6ffff models
> color #5 #e7c66bff models
> set bgColor white
> volume #7 level 0.02478
> volume #4 level 0.2097
> volume #2 level 0.2185
> surface dust #2 size 11
> surface dust #4 size 11
> surface dust #5 size 11
> surface dust #7 size 13.2
> surface dust #2 size 11
> surface dust #4 size 11
> surface dust #5 size 11
> surface dust #7 size 13.2
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> show #!5 models
> show #!7 models
> volume #7 level 0.02478
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!4 models
> show #!5 models
> volume #7 level 0.02496
> volume #4 level 0.2252
> volume #2 level 0.2185
> volume #7 level 0.03046
> hide #!2 models
> hide #!5 models
> volume #7 level 0.02826
> hide #!4 models
> volume #7 level 0.02918
> show #!4 models
> hide #!7 models
> volume #4 level 0.2319
> surface dust #4 size 11
> volume #4 level 0.1975
> show #!7 models
> hide #!4 models
> show #!4 models
> show #!5 models
> volume #5 level 7.63
> volume #5 level 6.799
> show #!2 models
> volume #4 level 0.2164
> lighting soft
> lighting simple
> hide #!5 models
> hide #!4 models
> hide #!7 models
> volume gaussin #2 sDev 2
Expected a density maps specifier or a keyword
> volume gaussian #2 sDev 2
Opened J1594_005_volume_map_sharp.mrc gaussian as #8, grid size 400,400,400,
pixel 1.1, shown at step 1, values float32
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> color #8 #e6bf99ff models
> color #8 #e66d99ff models
> color #8 #e66d50ff models
> volume #2 level 0.2439
> hide #!2 models
> volume #8 level 0.1873
> show #!5 models
> show #!4 models
> show #!7 models
> surface dust #4 size 11
> surface dust #5 size 11
> surface dust #7 size 13.2
> surface dust #8 size 11
> hide #!5 models
> hide #!7 models
> show #!7 models
> show #!5 models
> hide #!8 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!8 models
> hide #!7 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> save /Users/chenxi/Desktop/map-align.cxs includeMaps true
> open /Users/chenxi/Desktop/6kg7_9975.map
Opened 6kg7_9975.map as #9, grid size 320,320,320, pixel 1.4, shown at level
5.79, step 2, values float32
> show #!1 models
> hide #!4 models
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.98028,-0.0029889,0.19761,-43.715,-0.042495,0.97331,0.22552,-39.809,-0.19301,-0.22947,0.95399,109.85
> view matrix models
> #9,0.76917,-0.61221,0.18326,153.55,0.55355,0.78157,0.28761,-143.09,-0.31931,-0.11977,0.94005,115.35
> view matrix models
> #9,0.57186,-0.6004,0.55902,102.14,0.32757,0.79188,0.5154,-151.1,-0.75211,-0.11162,0.64951,282.51
> view matrix models
> #9,0.58535,-0.44808,0.67572,33.679,0.32717,0.89309,0.3088,-124.22,-0.74184,0.040318,0.66936,238.81
> view matrix models
> #9,0.77537,-0.43583,0.45701,42.113,0.43274,0.89374,0.11812,-100.96,-0.45993,0.10618,0.88158,107.16
> view matrix models
> #9,0.65329,-0.61432,0.44252,115.99,0.62209,0.76869,0.14873,-121.06,-0.43153,0.17812,0.88434,82.822
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.65329,-0.61432,0.44252,95.629,0.62209,0.76869,0.14873,-121.4,-0.43153,0.17812,0.88434,58.884
> view matrix models
> #9,0.65329,-0.61432,0.44252,63.472,0.62209,0.76869,0.14873,-139.24,-0.43153,0.17812,0.88434,67.932
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.69479,-0.63066,0.34573,82.003,0.62703,0.76662,0.13832,-137.28,-0.35227,0.12068,0.92809,53.093
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.69479,-0.63066,0.34573,97.647,0.62703,0.76662,0.13832,-130.65,-0.35227,0.12068,0.92809,44.153
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.73589,-0.5962,0.32094,86.263,0.63694,0.77035,-0.029421,-92.291,-0.2297,0.22607,0.94664,-13.289
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.73589,-0.5962,0.32094,84.4,0.63694,0.77035,-0.029421,-87.816,-0.2297,0.22607,0.94664,-12.536
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.74749,-0.65533,0.10858,148.5,0.65386,0.75471,0.053701,-108.42,-0.11714,0.030855,0.99264,-2.3376
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.74749,-0.65533,0.10858,162.49,0.65386,0.75471,0.053701,-119.02,-0.11714,0.030855,0.99264,-2.0256
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.63005,-0.76608,0.12711,210.89,0.76662,0.6397,0.055491,-117.19,-0.12383,0.062485,0.99033,-7.5478
> fitmap #9 inMap #1
Fit map 6kg7_9975.map in map J1551_009_volume_map_sharp.mrc using 40953 points
correlation = 0.6544, correlation about mean = 0.2271, overlap = 7.534e+04
steps = 228, shift = 13.6, angle = 8.05 degrees
Position of 6kg7_9975.map (#9) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.63115239 -0.77565794 -0.00119393 252.34440852
0.77565847 0.63115286 -0.00002573 -95.73975131
0.00077351 -0.00090984 0.99999929 -18.14137298
Axis -0.00056990 -0.00126823 0.99999903
Axis point 226.85809077 217.43861992 0.00000000
Rotation angle (degrees) 50.86481399
Shift along axis -18.16374702
> volume #9 step 1
> view matrix models
> #9,0.52427,-0.78822,0.32225,199.44,0.83893,0.543,-0.03667,-79.713,-0.14608,0.28957,0.94594,-41.602
> undo
> fitmap #9 inMap #1
Fit map 6kg7_9975.map in map J1551_009_volume_map_sharp.mrc using 327628
points
correlation = 0.6566, correlation about mean = 0.2319, overlap = 5.993e+05
steps = 248, shift = 0.0822, angle = 0.0681 degrees
Position of 6kg7_9975.map (#9) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.63147798 -0.77539370 -0.00040337 251.97013154
0.77539374 0.63147762 0.00075733 -95.98917390
-0.00033251 -0.00079101 0.99999963 -17.95444525
Axis -0.00099842 -0.00004569 0.99999950
Axis point 226.96063555 217.06646095 0.00000000
Rotation angle (degrees) 50.84077743
Shift along axis -18.20162315
> surface dust #9 size 14
> volume gaussian #9 sDev 2
Opened 6kg7_9975.map gaussian as #10, grid size 320,320,320, pixel 1.4, shown
at step 1, values float32
> select subtract #9
Nothing selected
> select add #10
2 models selected
> volume #10 level 9.858
> hide #!1 models
> volume #10 level 7.611
> color #10 #f3cc99ff models
> color #10 #f3a399ff models
> color #10 #f3a361ff models
> select subtract #10
Nothing selected
> undo
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> select subtract #10
Nothing selected
> hide #!9 models
> show #!7 models
> show #!4 models
> volume #10 level 11.19
> show #!2 models
> volume #10 level 8.941
> hide #!2 models
> open /Users/chenxi/Desktop/mP1-RH-detergent/RH-full-length/RH-detergent-
> composite_map-j126.ccp4
Opened RH-detergent-composite_map-j126.ccp4 as #11, grid size 400,400,400,
pixel 1.1, shown at level 5.1, step 2, values float32
> hide #!4 models
> hide #!10 models
> hide #!7 models
> close #9
> close #10
> show #!1 models
> hide #!1 models
> color #11 #f3b2b2ff models
> show #!1 models
> select add #11
2 models selected
> view matrix models
> #11,0.98858,0.071587,0.13262,-41.411,-0.13987,0.76347,0.63052,-62.516,-0.056115,-0.64187,0.76476,193.38
> view matrix models
> #11,0.84778,-0.44748,-0.28465,190.3,0.5064,0.52358,0.68514,-187.94,-0.15755,-0.725,0.67049,256.27
> view matrix models
> #11,0.35006,0.8921,-0.28568,50.992,0.9234,-0.27738,0.2653,-38.49,0.15743,-0.35667,-0.92087,468.34
> view matrix models
> #11,0.11347,0.92409,0.36495,-44.831,0.98502,-0.15264,0.080235,-36.084,0.12985,0.35038,-0.92756,337.98
> view matrix models
> #11,0.25987,0.96551,-0.016328,-2.4004,0.94155,-0.24959,0.22627,-39.547,0.21439,-0.074173,-0.97393,410.89
> view matrix models
> #11,0.14223,0.94743,0.28662,-38.697,0.96606,-0.19594,0.16831,-42.949,0.21563,0.25296,-0.94314,339.4
> view matrix models
> #11,0.10018,0.9297,0.35442,-40.243,0.98595,-0.14061,0.09016,-40.936,0.13366,0.34041,-0.93073,339.71
> ui mousemode right translate
> select subtract #11
Nothing selected
> select add #11
2 models selected
> hide #!11 models
> show #!11 models
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.014271,0.58554,0.81052,-55.295,0.99989,-0.0043575,-0.014458,-47.297,-0.0049339,0.81063,-0.58554,203.19
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.014271,0.58554,0.81052,-76.879,0.99989,-0.0043575,-0.014458,-29.983,-0.0049339,0.81063,-0.58554,200.41
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.83128,0.32449,0.45131,265.53,0.55298,0.56516,0.61221,-173.72,-0.056406,0.75848,-0.64925,237.89
> view matrix models
> #11,-0.96129,0.14269,0.23573,382.47,0.26923,0.66864,0.69314,-142.17,-0.05872,0.72977,-0.68117,251.36
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.96129,0.14269,0.23573,387.51,0.26923,0.66864,0.69314,-136.43,-0.05872,0.72977,-0.68117,241.39
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.96065,0.18529,0.20694,385.55,0.2756,0.72872,0.62691,-134.72,-0.034638,0.65927,-0.75111,265.18
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.96065,0.18529,0.20694,381.45,0.2756,0.72872,0.62691,-142.14,-0.034638,0.65927,-0.75111,264.48
> volume #11 step 1
> fitmap #11 inMap #1
Fit map RH-detergent-composite_map-j126.ccp4 in map
J1551_009_volume_map_sharp.mrc using 639691 points
correlation = 0.7624, correlation about mean = 0.2466, overlap = 1.165e+06
steps = 168, shift = 4.81, angle = 9.31 degrees
Position of RH-detergent-composite_map-j126.ccp4 (#11) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.92913867 0.32648052 0.17352750 347.90568690
0.35589036 0.66252072 0.65909661 -154.74942648
0.10021664 0.67414892 -0.73176490 220.16612431
Axis 0.18719119 0.91169738 0.36574218
Axis point 192.24943756 0.00000000 137.29540924
Rotation angle (degrees) 177.69576187
Shift along axis 4.56427180
> volume gaussian #11 sDev 2
Opened RH-detergent-composite_map-j126.ccp4 gaussian as #9, grid size
400,400,400, pixel 1.1, shown at step 1, values float32
> color #9 #f3ffb2ff models
> color #9 #f3a3b2ff models
> color #9 #f3a361ff models
> hide #!1 models
> volume #9 level 4.606
> volume #9 level 4.237
> select subtract #11
Nothing selected
> select add #9
2 models selected
> select subtract #9
Nothing selected
> show #!11 models
> hide #!9 models
> volume gaussian #11 sDev 1
Opened RH-detergent-composite_map-j126.ccp4 gaussian as #10, grid size
400,400,400, pixel 1.1, shown at step 1, values float32
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> volume #10 level 8.433
> hide #!10 models
> show #!11 models
> volume #11 level 5.587
> volume #11 level 10.63
> show #!10 models
> hide #!11 models
> show #!7 models
> show #!9 models
> volume #9 level 7.005
> hide #!10 models
> volume #9 level 7.65
> hide #!9 models
> show #!10 models
> color #10 #f3ffffff models
> color #10 #f3a3ffff models
> color #10 #f3a361ff models
> volume #10 level 10.7
> surface dust #7 size 13.2
> surface dust #10 size 11
> volume #10 level 11.64
> volume #10 level 11.87
> hide #!10 models
> show #!9 models
> volume #9 level 7.374
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #11 level 10.87
> hide #!11 models
> close #10
> volume #9 level 8.342
> surface dust #7 size 13.2
> surface dust #9 size 11
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #9 level 7.558
> show #!11 models
> hide #!11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> volume #9 level 5.713
> show #!8 models
> hide #!9 models
> show #!9 models
> show #!7 models
> hide #!8 models
> volume #9 level 7.281
> show #!4 models
> hide #!7 models
> hide #!9 models
> save /Users/chenxi/Desktop/map-align.cxs includeMaps true
——— End of log from Sun Aug 17 02:57:48 2025 ———
opened ChimeraX session
> open /Users/chenxi/Desktop/RH-figure/RH_patfla_J76_006_volume_map_sharp.mrc
Opened RH_patfla_J76_006_volume_map_sharp.mrc as #10, grid size 196,196,196,
pixel 2.2, shown at level 0.636, step 1, values float32
> ui tool show "Map Filter"
> show #!1 models
> hide #!1 models
> close #4
> close #5
> close #7
> close #8
> close #9
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select add #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.53839,0.84024,0.064283,157.83,0.84063,0.54084,-0.028758,-87.584,-0.058931,0.038555,-0.99752,426.09
> view matrix models
> #10,-0.53765,0.84244,0.035035,163.35,0.84304,0.53783,0.0048557,-94.566,-0.014752,0.032146,-0.99937,417.7
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.53765,0.84244,0.035035,150.17,0.84304,0.53783,0.0048557,-77.003,-0.014752,0.032146,-0.99937,449.66
> fitmap #10 inMap #1
Fit map RH_patfla_J76_006_volume_map_sharp.mrc in map
J1551_009_volume_map_sharp.mrc using 75235 points
correlation = 0.8115, correlation about mean = 0.4768, overlap = 1.653e+04
steps = 116, shift = 3.67, angle = 6.48 degrees
Position of RH_patfla_J76_006_volume_map_sharp.mrc (#10) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.62523727 0.78043469 0.00021827 186.12981972
0.78043460 0.62523730 -0.00038317 -82.81178347
-0.00043551 -0.00006923 -0.99999990 453.77261586
Axis 0.43287574 0.90145359 -0.00012553
Axis point 112.99354916 0.00000000 226.86207898
Rotation angle (degrees) 179.97922307
Shift along axis 5.86314365
> select subtract #10
Nothing selected
> open /Users/chenxi/Desktop/mP1-WT-GSMTx4/J110_map_j75fliphand.mrc
Opened J110_map_j75fliphand.mrc as #4, grid size 384,384,384, pixel 1.1, shown
at level 0.237, step 2, values float32
> hide #!10 models
> volume #4 step 1
> volume #4 level 0.2395
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.31876,-0.94706,0.038372,321.4,0.94305,0.32096,0.087389,-85.55,-0.095078,0.0083309,0.99543,19.483
> select subtract #4
Nothing selected
> hide #!1 models
> volume #4 level 0.2638
> show #!1 models
> select add #4
2 models selected
> view matrix models
> #4,0.3407,-0.93957,0.033659,316.4,0.93307,0.3423,0.11049,-92.857,-0.11534,-0.0062384,0.99331,27.059
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.3407,-0.93957,0.033659,328.36,0.93307,0.3423,0.11049,-88.09,-0.11534,-0.0062384,0.99331,49.042
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.30343,-0.94901,-0.085568,364.61,0.95204,0.29824,0.06833,-73.898,-0.039326,-0.1022,0.99399,52.076
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.30343,-0.94901,-0.085568,366.45,0.95204,0.29824,0.06833,-66.411,-0.039326,-0.1022,0.99399,48.939
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.51437,-0.85671,-0.038404,293.75,0.85753,0.51426,0.013249,-77.225,0.0083992,-0.039747,0.99917,25.482
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.51437,-0.85671,-0.038404,289.87,0.85753,0.51426,0.013249,-62.422,0.0083992,-0.039747,0.99917,25.761
> close #4
> open /Users/chenxi/Desktop/mP1-WT-GSMTx4/J75_011_volume_map.mrc
Opened J75_011_volume_map.mrc as #4, grid size 384,384,384, pixel 1.1, shown
at level 0.237, step 2, values float32
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.79347,-0.4792,0.37519,76.139,-0.57333,-0.79539,0.19661,485.74,0.2042,-0.37111,-0.90586,423.15
> view matrix models
> #4,0.73289,-0.55103,0.39905,100.27,-0.65622,-0.72736,0.20081,486.95,0.1796,-0.40903,-0.89467,434.62
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.73289,-0.55103,0.39905,103.2,-0.65622,-0.72736,0.20081,469.37,0.1796,-0.40903,-0.89467,436.94
> view matrix models
> #4,0.73289,-0.55103,0.39905,89.787,-0.65622,-0.72736,0.20081,474.36,0.1796,-0.40903,-0.89467,460.17
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.76922,-0.63398,-0.079793,196.92,-0.63635,-0.77138,-0.0057159,521.55,-0.057926,0.055173,-0.9968,425.83
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.76922,-0.63398,-0.079793,201.49,-0.63635,-0.77138,-0.0057159,527.1,-0.057926,0.055173,-0.9968,442.47
> fitmap #4 inMap #1
Fit map J75_011_volume_map.mrc in map J1551_009_volume_map_sharp.mrc using
70615 points
correlation = 0.846, correlation about mean = 0.577, overlap = 5012
steps = 180, shift = 11.3, angle = 5.31 degrees
Position of J75_011_volume_map.mrc (#4) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.74153473 -0.67091430 0.00049103 204.61614577
-0.67091438 -0.74153483 -0.00001246 517.32913807
0.00037248 -0.00032020 -0.99999988 442.17680337
Axis -0.93314975 0.35948783 -0.00023148
Axis point 0.00000000 298.09739838 221.04008852
Rotation angle (degrees) 179.99055244
Shift along axis -5.06633237
> select subtract #4
Nothing selected
> hide #!1 models
> volume #4 level 0.2748
> volume #4 step 1
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> surface dust #6 size 13.2
> volume #6 lowpass 4
Expected a keyword
> volume #6 low pass 4
Expected a keyword
> ui tool show "Map Filter"
[Repeated 1 time(s)]
> volume fourier #6 low pass 4
Expected a keyword
> volume fourier #6 lowpass 4
Expected a keyword
> vop fourier #6 lowpass 4
> volume fourier #6 lowpass 4
Expected a keyword
> volume filter #1 fourier lowpass 10 newMap true name #1_lp10
Expected a density maps specifier or a keyword
> ui tool show "Map Filter"
> volume fourier #6
Opened 5z10.map FT as #5, grid size 280,280,280, pixel 1.32, shown at step 1,
values float32
> volume #5 level 5.143e-06
> close #5
> show #!1 models
> volume #1 filter 10
Expected a keyword
> volume filter #1 10
Expected a density maps specifier or a keyword
> help help:user/tools/mapfilter.html
> volume fourier #1 10
Expected a keyword
> show #!10 models
> hide #!10 models
> ui tool show "Volume Viewer"
> volume fourier #1 10
Expected a keyword
> volume fourier #1 fliter 10
Expected a keyword
> volume fourier #1
Opened J1551_009_volume_map_sharp.mrc FT as #5, grid size 400,400,400, pixel
1.1, shown at step 1, values float32
> volume #5 level 6.692e-05
> close #5
> show #!1 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> surface dust #1 size 11
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.2723
> volume #4 level 0.2359
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> volume #4 level 0.3039
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #6 level 0.0441
> surface dust #6 size 13.2
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.2578
> volume #4 level 0.3087
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.2602
> hide #!6 models
> open /Users/chenxi/Desktop/mP1-RH-detergent/RH-full-length/RH-detergent-
> composite_map-j126.ccp4
Opened RH-detergent-composite_map-j126.ccp4 as #5, grid size 400,400,400,
pixel 1.1, shown at level 5.1, step 2, values float32
> hide #11.1 models
> show #!11 models
> close #11
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!10 models
> hide #!10 models
> open /Users/chenxi/Desktop/mP1-WT-GSMTx4/切整个blade-
> postprocess_masked_job217_blade.mrc
Opened 切整个blade-postprocess_masked_job217_blade.mrc as #7, grid size
192,192,192, pixel 2.2, shown at level 0.0286, step 1, values float32
> volume #7 level 0.03311
> volume #7 step 8
> volume #7 step 2
> volume #7 step 1
> surface dust #7 size 22
> show #!6 models
> hide #!6 models
> volume flip #7
Opened 切整个blade-postprocess_masked_job217_blade.mrc z flip as #8, grid size
192,192,192, pixel 2.2, shown at step 1, values float32
> show #!6 models
> select add #8
2 models selected
> view matrix models #8,1,0,0,13.362,0,1,0,9.9457,0,0,1,1.5911
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.96942,-0.24519,-0.0099679,76.981,0.24536,0.96916,0.023144,-41.342,0.0039859,-0.024882,0.99968,6.3605
> view matrix models
> #8,0.96952,-0.24408,-0.021187,79.339,0.24462,0.96922,0.028003,-42.333,0.0137,-0.032333,0.99938,6.0047
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.96952,-0.24408,-0.021187,74.155,0.24462,0.96922,0.028003,-42.351,0.0137,-0.032333,0.99938,5.4967
> fitmap #8 inMap #6
Fit map 切整个blade-postprocess_masked_job217_blade.mrc z flip in map 5z10.map
using 40189 points
correlation = 0.7702, correlation about mean = 0.5933, overlap = 58.76
steps = 128, shift = 9.53, angle = 2.13 degrees
Position of 切整个blade-postprocess_masked_job217_blade.mrc z flip (#8) relative
to 5z10.map (#6) coordinates:
Matrix rotation and translation
0.98636359 0.16458035 0.00042898 -57.96380598
-0.16458038 0.98636368 0.00002487 11.56006259
-0.00041904 -0.00009513 0.99999991 -25.21907243
Axis -0.00036454 0.00257630 -0.99999661
Axis point 40.39053608 355.48214614 0.00000000
Rotation angle (degrees) 9.47289013
Shift along axis 25.26989966
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> surface dust #6 size 13.2
> surface dust #8 size 22
> hide #!8 models
> hide #!6 models
> open /Users/chenxi/Desktop/low1/5z10_low5.mrc
Opened 5z10_low5.mrc as #9, grid size 280,280,280, pixel 1.32, shown at level
0.0256, step 2, values float32
> volume #9 step 1
> volume #9 level 0.04406
> surface dust #9 size 13.2
> show #!1 models
> color #9 #b24ab2ff models
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.96569,-0.16305,-0.20212,80.119,0.069188,0.91173,-0.40492,88.525,0.2503,0.37704,0.89173,-97.315
> view matrix models
> #9,0.9965,-0.08221,-0.015408,20.031,0.081235,0.99513,-0.055773,-2.228,0.019918,0.054326,0.99832,-13.974
> view matrix models
> #9,0.91388,-0.40549,-0.020038,99.702,0.40534,0.9141,-0.011334,-54.109,0.022913,0.0022355,0.99973,-4.5348
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.91388,-0.40549,-0.020038,135.43,0.40534,0.9141,-0.011334,-17.704,0.022913,0.0022355,0.99973,2.5196
> view matrix models
> #9,0.91388,-0.40549,-0.020038,131.66,0.40534,0.9141,-0.011334,-22.158,0.022913,0.0022355,0.99973,33.865
> fitmap #9 inMap #1
Fit map 5z10_low5.mrc in map J1551_009_volume_map_sharp.mrc using 64694 points
correlation = 0.8223, correlation about mean = 0.4805, overlap = 1489
steps = 56, shift = 3.08, angle = 1.31 degrees
Position of 5z10_low5.mrc (#9) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.91403311 -0.40563958 0.00003895 125.60724658
0.40563958 0.91403307 -0.00028391 -24.20951654
0.00007957 0.00027530 0.99999996 35.85537655
Axis 0.00068930 -0.00005006 0.99999976
Axis point 119.90399992 284.18009972 0.00000000
Rotation angle (degrees) 23.93121879
Shift along axis 35.94316091
> select subtract #9
Nothing selected
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!1 models
> volume #9 level 0.03908
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> open /Users/chenxi/Desktop/low1/8IXO-35800_low8.mrc
Opened 8IXO-35800_low8.mrc as #11, grid size 368,368,368, pixel 1.1, shown at
level 5.8, step 2, values float32
> volume #11 level 6.842
> open /Users/chenxi/Desktop/low1/RH_patfla_J76_006_volume_map_sharp_low8.mrc
Opened RH_patfla_J76_006_volume_map_sharp_low8.mrc as #12, grid size
196,196,196, pixel 2.2, shown at level 0.619, step 1, values float32
> volume #12 level 0.8007
> open /Users/chenxi/Desktop/low1/RH-detergent-composite_map-j126_low8.mrc
Opened RH-detergent-composite_map-j126_low8.mrc as #13, grid size 400,400,400,
pixel 1.1, shown at level 5.01, step 2, values float32
> volume #13 level 5.475
> show #!2 models
> volume #2 level 0.2946
> volume #2 level 0.3344
> hide #!13 models
> hide #!12 models
> hide #!11 models
> volume #2 level 0.2366
> show #!1 models
> hide #!2 models
> show #!13 models
> select add #13
2 models selected
> view matrix models #13,1,0,0,13.225,0,1,0,-24.775,0,0,1,1.9624
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.38422,0.56702,0.7286,-138.76,0.3475,0.64233,-0.68312,135.99,-0.85535,0.51566,0.04976,331.94
> view matrix models
> #13,-0.45715,-0.55826,0.69236,284.58,0.34011,0.60956,0.71607,-203.44,-0.82179,0.56283,-0.088793,349.38
> view matrix models
> #13,-0.35603,-0.62365,0.69592,273.47,0.48411,0.51389,0.7082,-215.56,-0.7993,0.58905,0.11895,287.46
> show #!5 models
> hide #!5 models
> view matrix models
> #13,-0.28097,-0.65595,0.70056,261.52,0.80769,0.23265,0.54177,-192.75,-0.51835,0.71806,0.46444,111.95
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.28097,-0.65595,0.70056,103.75,0.80769,0.23265,0.54177,-293.84,-0.51835,0.71806,0.46444,95.425
> show #!3 models
> hide #!3 models
> show #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.29265,-0.6107,0.7358,88.738,0.86161,0.16532,0.47989,-277.52,-0.41471,0.77441,0.47781,57.285
> select add #5
4 models selected
> view matrix models
> #5,0.99097,-0.018041,-0.13285,36.575,0.02066,0.99962,0.018366,-12.16,0.13247,-0.020945,0.99097,-11.568,#13,-0.25045,-0.71105,0.65702,121.91,0.84762,0.16686,0.50369,-286.69,-0.46778,0.68305,0.56091,62.767
> select subtract #13
2 models selected
> view matrix models
> #5,-0.98888,0.12084,0.086642,449.67,0.12624,0.37441,0.91863,-120.63,0.078568,0.91936,-0.3855,130.71
> hide #!5 models
> select subtract #5
Nothing selected
> volume flip #13
Opened RH-detergent-composite_map-j126_low8.mrc z flip as #14, grid size
400,400,400, pixel 1.1, shown at step 1, values float32
> select add #14
2 models selected
> view matrix models
> #14,0.067174,-0.11234,-0.9914,244.28,-0.66082,-0.74947,0.04015,327.06,-0.74753,0.65244,-0.12458,262.99
> view matrix models
> #14,0.24949,0.0060785,-0.96836,174.85,-0.67967,-0.7112,-0.17958,365.56,-0.68979,0.70297,-0.17331,249.07
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.24949,0.0060785,-0.96836,325.92,-0.67967,-0.7112,-0.17958,535.31,-0.68979,0.70297,-0.17331,344.7
> view matrix models
> #14,0.24949,0.0060785,-0.96836,353.27,-0.67967,-0.7112,-0.17958,556.2,-0.68979,0.70297,-0.17331,260.55
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.091107,0.20798,-0.97388,350.74,-0.69499,-0.68713,-0.21176,561.07,-0.71322,0.69613,0.081941,218.78
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.091107,0.20798,-0.97388,326.37,-0.69499,-0.68713,-0.21176,557.62,-0.71322,0.69613,0.081941,223.99
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.3903,0.51924,-0.76029,156,-0.56531,-0.51664,-0.64305,576.25,-0.7267,0.68078,0.091887,228.21
> view matrix models
> #14,0.41588,0.54491,-0.72809,138.97,-0.54476,-0.49181,-0.67923,573.53,-0.7282,0.67912,0.09231,228.8
> view matrix models
> #14,0.4356,0.52207,-0.73328,139.95,-0.43045,-0.59463,-0.67906,567.62,-0.79055,0.61144,-0.034301,280.46
> fitmap #14 inMap #1
Fit map RH-detergent-composite_map-j126_low8.mrc z flip in map
J1551_009_volume_map_sharp.mrc using 547855 points
correlation = 0.7641, correlation about mean = 0.1492, overlap = 9.109e+05
steps = 124, shift = 11.1, angle = 7.87 degrees
Position of RH-detergent-composite_map-j126_low8.mrc z flip (#14) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47757278 0.40260606 -0.78091780 174.38864755
-0.48677829 -0.61869033 -0.61665969 570.75689491
-0.73141722 0.67463371 -0.09948977 263.43739378
Axis 0.82314913 -0.03155469 -0.56694780
Axis point 0.00000000 215.22947135 359.38051849
Rotation angle (degrees) 128.33831281
Shift along axis -23.81744429
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> hide #!14 models
> show #!12 models
> select add #12
2 models selected
> view matrix models
> #12,0.45894,0.88708,-0.049698,-54.067,0.86461,-0.43304,0.25482,52.695,0.20452,-0.15992,-0.96571,401.75
> view matrix models
> #12,0.97754,0.18541,0.10017,-55.211,0.15617,-0.95651,0.24637,326.18,0.1415,-0.2252,-0.96398,429.51
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.97754,0.18541,0.10017,-51.831,0.15617,-0.95651,0.24637,334.11,0.1415,-0.2252,-0.96398,466.71
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.9897,0.14284,-0.009105,-22.557,0.14203,-0.97223,0.18602,353.38,0.01772,-0.1854,-0.9825,490.34
> view matrix models
> #12,0.98185,0.16755,0.08885,-46.647,0.15545,-0.97938,0.12905,363.85,0.10864,-0.1129,-0.98765,455.43
> view matrix models
> #12,0.97979,0.17325,0.09995,-49.725,0.16139,-0.97998,0.11655,365.26,0.11814,-0.09806,-0.98814,450.24
> view matrix models
> #12,0.97935,0.193,0.060188,-45.417,0.19319,-0.98116,0.0027331,382.28,0.059581,0.0089511,-0.99818,443.04
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.97935,0.193,0.060188,-41.977,0.19319,-0.98116,0.0027331,384.56,0.059581,0.0089511,-0.99818,442.66
> fitmap #12 inMap #1
Fit map RH_patfla_J76_006_volume_map_sharp_low8.mrc in map
J1551_009_volume_map_sharp.mrc using 35288 points
correlation = 0.8111, correlation about mean = 0.4405, overlap = 1.156e+04
steps = 68, shift = 6.2, angle = 4.22 degrees
Position of RH_patfla_J76_006_volume_map_sharp_low8.mrc (#12) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98843568 0.15164070 -0.00006626 -25.72160077
0.15164070 -0.98843568 -0.00002846 399.65116172
-0.00006981 0.00001808 -1.00000000 453.93709288
Axis 0.99710456 0.07604268 -0.00002983
Axis point 0.00000000 200.80373453 226.97049793
Rotation angle (degrees) 179.99866296
Shift along axis 4.72988020
> select subtract #12
Nothing selected
> hide #!12 models
> show #!11 models
> select add #11
2 models selected
> view matrix models #11,1,0,0,3.3249,0,1,0,1.9531,0,0,1,7.1998
> view matrix models #11,1,0,0,4.7164,0,1,0,2.495,0,0,1,5.3923
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.093762,-0.55441,-0.82695,533.99,-0.4566,0.76205,-0.45913,248.6,0.88472,0.33454,-0.32459,17.528
> view matrix models
> #11,-0.12387,-0.064088,-0.99023,466.43,-0.43479,0.90052,-0.0038929,118.6,0.89197,0.43006,-0.13941,-43.641
> volume flip #11
Opened 8IXO-35800_low8.mrc z flip as #15, grid size 368,368,368, pixel 1.1,
shown at step 1, values float32
> select subtract #11
Nothing selected
> select add #15
2 models selected
> view matrix models
> #15,-0.1077,-0.36184,-0.926,516.03,-0.4493,0.84859,-0.27933,186.78,0.88686,0.38597,-0.25397,-10.532
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.1077,-0.36184,-0.926,505.12,-0.4493,0.84859,-0.27933,207.42,0.88686,0.38597,-0.25397,-2.3908
> view matrix models
> #15,-0.1077,-0.36184,-0.926,508.91,-0.4493,0.84859,-0.27933,197.04,0.88686,0.38597,-0.25397,27.939
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.030636,-0.34778,-0.93708,478.28,-0.45974,0.82756,-0.32216,212.25,0.88752,0.44068,-0.13454,-7.5042
> view matrix models
> #15,-0.15212,-0.34263,-0.92707,514.43,-0.29955,0.90986,-0.28711,152.91,0.94187,0.23403,-0.24104,47.075
> view matrix models
> #15,-0.17431,-0.16143,-0.97137,487.91,-0.29186,0.95061,-0.1056,106.95,0.94044,0.26509,-0.21282,35.046
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.17431,-0.16143,-0.97137,487.77,-0.29186,0.95061,-0.1056,117.1,0.94044,0.26509,-0.21282,36.926
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.053145,-0.14636,-0.9878,461.64,-0.23078,0.96422,-0.13045,105.83,0.97155,0.22104,-0.085022,15.069
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.11972,-0.10207,-0.98755,466.12,-0.066046,0.99332,-0.094663,57.085,0.99061,0.05389,-0.12566,55.702
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.11972,-0.10207,-0.98755,470.48,-0.066046,0.99332,-0.094663,52.265,0.99061,0.05389,-0.12566,47.827
> fitmap #15 inMap #1
Fit map 8IXO-35800_low8.mrc z flip in map J1551_009_volume_map_sharp.mrc using
267666 points
correlation = 0.6037, correlation about mean = 0.1879, overlap = 4.104e+05
steps = 184, shift = 4.68, angle = 9.2 degrees
Position of 8IXO-35800_low8.mrc z flip (#15) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.03641827 -0.23100764 -0.97227012 471.06680365
-0.03284356 0.97266661 -0.22987162 77.40268170
0.99879678 0.02356129 -0.04300995 36.85860016
Axis 0.12689738 -0.98694060 0.09922351
Axis point 222.19041518 0.00000000 249.34312105
Rotation angle (degrees) 93.05994937
Shift along axis -12.95746614
> select subtract #15
Nothing selected
> hide #!15 models
> show #!8 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!9 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.03486
> surface dust #8 size 22
> surface dust #9 size 13.2
> volume #8 level 0.04291
> volume #8 level 0.03556
> hide #!9 models
> volume #8 level 0.03346
> volume #8 level 0.03416
> show #!9 models
> hide #!8 models
> volume #9 level 0.03553
> volume #9 level 0.0334
> volume #8 level 0.034
> volume #9 level 0.034
> show #!8 models
> show #!6 models
> hide #!9 models
> volume #8 level 0.0172
> volume #8 level 0.03295
> open /Users/chenxi/Desktop/mP1-WT-GSMTx4/切远端blade-run_class001_job348.mrc
Opened 切远端blade-run_class001_job348.mrc as #16, grid size 192,192,192, pixel
2.2, shown at level 0.0279, step 1, values float32
> volume #16 level 0.03089
> close #16
> show #!9 models
> volume #8 level 0.03435
> volume #8 level 0.034
> hide #!6 models
> show #!6 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> volume #6 level 0.04592
> show #!9 models
> hide #!6 models
> volume #9 level 0.03969
> volume #9 level 0.03329
[Repeated 1 time(s)]
> show #!6 models
> volume #6 level 0.03955
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!6 models
> show #!9 models
> show #!8 models
> volume #9 level 0.03969
> hide #!8 models
> volume #9 level 0.04253
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!6 models
> volume #6 level 0.04501
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> volume #4 level 0.2723
> volume #4 level 0.2966
> hide #!8 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> volume #9 level 0.04537
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.0361
[Repeated 1 time(s)]
> volume #9 level 0.04324
> volume #8 level 0.0368
> volume #9 level 0.04324
> volume #9 level 0.04111
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.034
> transparency #8.1#9.1 50
> transparency #8.1#9.1 0
> select add #8
2 models selected
> transparency sel 50
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color #9 #9bbf8aff models
> lighting soft
> select add #8
2 models selected
> transparency sel 0
> select subtract #8
Nothing selected
> lighting simple
> color #8 #82afda80 models
> transparency #8.1#9.1 0
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.03295
> color #9 #8ab07cff models
> volume #8 level 0.0347
> hide #!8 models
> show #!8 models
> color #8 #82afedff models
> color #8 #82afd5ff models
> color #8 #82afefff models
> color #8 #99afefff models
> color #8 #79afefff models
> color #8 #8dafefff models
> color #8 #acafefff models
> color #8 #98afefff models
> color #8 #80afefff models
> color #8 #669abaff models
> color #8 #377eb8ff models
> select add #8
2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel light gray
> color sel dark gray
> color sel dim gray
> color sel steel blue
> color sel cornflower blue
> color sel light steel blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel cornflower blue
> select subtract #8
Nothing selected
> select add #8
2 models selected
> hide #!9 models
> hide #!8 models
> show #!14 models
> show #!12 models
> select subtract #8
Nothing selected
> show #!2 models
> volume #14 level 8.02
> surface dust #2 size 11
> surface dust #12 size 22
> surface dust #14 size 11
> show #!8 models
> hide #!2 models
> show #!2 models
> hide #!14 models
> hide #!12 models
> hide #!2 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!1 models
> hide #!1 models
> hide #!14 models
> show #!13 models
> show #!8 models
> hide #!8 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!2 models
> show #!8 models
> fitmap #2 inMap #8
Fit map J1594_005_volume_map_sharp.mrc in map 切整个blade-
postprocess_masked_job217_blade.mrc z flip using 321152 points
correlation = 0.6558, correlation about mean = 0.2606, overlap = 2077
steps = 68, shift = 0.912, angle = 1.9 degrees
Position of J1594_005_volume_map_sharp.mrc (#2) relative to 切整个blade-
postprocess_masked_job217_blade.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.96185095 -0.27357273 -0.00083522 482.25432837
-0.27357033 0.96184937 -0.00224901 60.11706788
0.00141863 -0.00193472 -0.99999712 477.40329620
Axis 0.13810909 -0.99041646 0.00105604
Axis point 245.18157795 0.00000000 238.87190636
Rotation angle (degrees) 179.93480713
Shift along axis 7.56693029
> fitmap #2 inMap #8
Fit map J1594_005_volume_map_sharp.mrc in map 切整个blade-
postprocess_masked_job217_blade.mrc z flip using 321152 points
correlation = 0.6557, correlation about mean = 0.2611, overlap = 2077
steps = 40, shift = 0.0318, angle = 0.0191 degrees
Position of J1594_005_volume_map_sharp.mrc (#2) relative to 切整个blade-
postprocess_masked_job217_blade.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.96181707 -0.27369143 -0.00096413 482.30487213
-0.27368920 0.96181617 -0.00196780 60.07768645
0.00146589 -0.00162879 -0.99999760 477.35546446
Axis 0.13817026 -0.99040808 0.00090784
Axis point 245.19528941 0.00000000 238.85429565
Rotation angle (degrees) 179.92971082
Shift along axis 7.57212636
> hide #!8 models
> hide #!2 models
> show #!1 models
> show #!8 models
> fitmap #1 inMap #8
Fit map J1551_009_volume_map_sharp.mrc in map 切整个blade-
postprocess_masked_job217_blade.mrc z flip using 172515 points
correlation = 0.8611, correlation about mean = 0.4871, overlap = 2956
steps = 64, shift = 0.588, angle = 1.1 degrees
Position of J1551_009_volume_map_sharp.mrc (#1) relative to 切整个blade-
postprocess_masked_job217_blade.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.96251678 0.27122212 0.00012331 -60.12539014
-0.27122212 0.96251678 -0.00007452 59.02872497
-0.00013890 0.00003829 0.99999999 -11.11290976
Axis 0.00020797 0.00048338 -0.99999986
Axis point 183.47755619 247.04856016 0.00000000
Rotation angle (degrees) 15.73700522
Shift along axis 11.12893702
> hide #!8 models
> show #!9 models
> fitmap #1 inMap #9
Fit map J1551_009_volume_map_sharp.mrc in map 5z10_low5.mrc using 172515
points
correlation = 0.813, correlation about mean = 0.4387, overlap = 3124
steps = 64, shift = 0.611, angle = 0.998 degrees
Position of J1551_009_volume_map_sharp.mrc (#1) relative to 5z10_low5.mrc (#9)
coordinates:
Matrix rotation and translation
0.91332851 0.40722356 0.00007752 -105.17447710
-0.40722346 0.91332838 -0.00057047 73.83704032
-0.00030311 0.00048946 0.99999983 -35.93741404
Axis 0.00130141 0.00046735 -0.99999904
Axis point 120.81067653 284.09936369 0.00000000
Rotation angle (degrees) 24.03056327
Shift along axis 35.83501247
> hide #!9 models
> show #!8 models
> fitmap #1 inMap #8
Fit map J1551_009_volume_map_sharp.mrc in map 切整个blade-
postprocess_masked_job217_blade.mrc z flip using 172515 points
correlation = 0.8611, correlation about mean = 0.4876, overlap = 2957
steps = 64, shift = 0.597, angle = 0.994 degrees
Position of J1551_009_volume_map_sharp.mrc (#1) relative to 切整个blade-
postprocess_masked_job217_blade.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.96252664 0.27118707 -0.00020758 -60.01587956
-0.27118714 0.96252652 -0.00048419 59.15284428
0.00006850 0.00052234 0.99999986 -11.25320717
Axis 0.00185577 -0.00050903 -0.99999815
Axis point 184.04069702 246.81531912 0.00000000
Rotation angle (degrees) 15.73494885
Shift along axis 11.11170004
> hide #!8 models
> show #!2 models
> fitmap #1 inMap #2
Fit map J1551_009_volume_map_sharp.mrc in map J1594_005_volume_map_sharp.mrc
using 172515 points
correlation = 0.6456, correlation about mean = 0.2842, overlap = 1.354e+04
steps = 108, shift = 0.574, angle = 1.36 degrees
Position of J1551_009_volume_map_sharp.mrc (#1) relative to
J1594_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.86359012 -0.50419343 -0.00104967 520.23333457
-0.50419380 0.86359053 0.00010952 140.63098220
0.00085126 0.00062382 -0.99999945 487.57689898
Axis 0.26115996 -0.96529552 -0.00018997
Axis point 279.01613271 0.00000000 243.90727471
Rotation angle (degrees) 179.94358433
Shift along axis 0.02103773
> hide #!2 models
> show #!2 models
> fitmap #1 inMap #2
Fit map J1551_009_volume_map_sharp.mrc in map J1594_005_volume_map_sharp.mrc
using 172515 points
correlation = 0.6456, correlation about mean = 0.2841, overlap = 1.354e+04
steps = 116, shift = 0.012, angle = 0.0107 degrees
Position of J1551_009_volume_map_sharp.mrc (#1) relative to
J1594_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.86359316 -0.50418780 -0.00123516 520.28831345
-0.50418831 0.86359373 0.00012324 140.63136131
0.00100455 0.00072918 -0.99999923 487.51561421
Axis 0.26115694 -0.96529633 -0.00022080
Axis point 279.02129727 0.00000000 243.89804542
Rotation angle (degrees) 179.93353026
Shift along axis 0.01832410
> show #!8 models
> hide #!2 models
> select add #8
2 models selected
> fitmap #8 inMap #1
Fit map 切整个blade-postprocess_masked_job217_blade.mrc z flip in map
J1551_009_volume_map_sharp.mrc using 33254 points
correlation = 0.8169, correlation about mean = 0.5313, overlap = 449.2
steps = 92, shift = 0.486, angle = 1.2 degrees
Position of 切整个blade-postprocess_masked_job217_blade.mrc z flip (#8) relative
to J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.96323910 -0.26864547 -0.00020357 73.19901919
0.26864548 0.96323912 0.00005125 -40.11463797
0.00018232 -0.00010406 0.99999998 11.02095589
Axis -0.00028906 -0.00071822 0.99999970
Axis point 183.14940087 247.42450000 0.00000000
Rotation angle (degrees) 15.58368552
Shift along axis 11.02860486
> show #!2 models
> select add #2
4 models selected
> hide #!8 models
> select subtract #8
2 models selected
> fitmap #2 inMap #1
Fit map J1594_005_volume_map_sharp.mrc in map J1551_009_volume_map_sharp.mrc
using 321152 points
correlation = 0.4959, correlation about mean = 0.1729, overlap = 1.37e+04
steps = 68, shift = 0.659, angle = 0.664 degrees
Position of J1594_005_volume_map_sharp.mrc (#2) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.86894068 -0.49491597 -0.00051610 519.16097675
-0.49491151 0.86893646 -0.00346770 138.16139780
0.00216468 -0.00275780 -0.99999385 487.37091169
Axis 0.25598648 -0.96667902 0.00161000
Axis point 277.69899318 0.00000000 243.98666738
Rotation angle (degrees) 179.92055403
Shift along axis 0.12513007
> hide #!2 models
> select subtract #2
Nothing selected
> show #!8 models
> select add #8
2 models selected
> fitmap #8 inMap #1
Fit map 切整个blade-postprocess_masked_job217_blade.mrc z flip in map
J1551_009_volume_map_sharp.mrc using 33254 points
correlation = 0.8169, correlation about mean = 0.5313, overlap = 449.2
steps = 24, shift = 0.00811, angle = 0.00819 degrees
Position of 切整个blade-postprocess_masked_job217_blade.mrc z flip (#8) relative
to J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.96324157 -0.26863670 -0.00008475 73.16742762
0.26863670 0.96324157 -0.00002766 -40.10275979
0.00008906 0.00000388 1.00000000 11.01706703
Axis 0.00005870 -0.00032350 0.99999995
Axis point 183.10915527 247.30788116 0.00000000
Rotation angle (degrees) 15.58315972
Shift along axis 11.03433468
> hide #!8 models
> select subtract #8
Nothing selected
> show #!9 models
> select add #9
2 models selected
> fitmap #9 inMap #1
Fit map 5z10_low5.mrc in map J1551_009_volume_map_sharp.mrc using 75416 points
correlation = 0.8164, correlation about mean = 0.481, overlap = 1578
steps = 64, shift = 0.181, angle = 0.357 degrees
Position of 5z10_low5.mrc (#9) relative to J1551_009_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.91402160 -0.40566511 0.00057812 125.48732713
0.40566541 0.91402147 -0.00056523 -24.14780526
-0.00029912 0.00075116 0.99999967 35.84229558
Axis 0.00162250 0.00108123 0.99999810
Axis point 119.77389474 283.80778748 0.00000000
Rotation angle (degrees) 23.93287083
Shift along axis 36.01972150
> hide #!9 models
> select subtract #9
Nothing selected
> show #!11 models
> select add #11
2 models selected
> view matrix models
> #11,-0.12387,-0.064088,-0.99023,453.48,-0.43479,0.90052,-0.0038929,134.02,0.89197,0.43006,-0.13941,-5.4702
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.2373,-0.073691,-0.96864,475.46,-0.22799,0.97349,-0.018206,76.51,0.9443,0.21652,-0.24781,52.912
> hide #!11 models
> select subtract #11
Nothing selected
> show #!15 models
> select add #15
2 models selected
> fitmap #15 inMap #1
Fit map 8IXO-35800_low8.mrc z flip in map J1551_009_volume_map_sharp.mrc using
267666 points
correlation = 0.6038, correlation about mean = 0.1881, overlap = 4.104e+05
steps = 32, shift = 0.178, angle = 0.344 degrees
Position of 8IXO-35800_low8.mrc z flip (#15) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.03641232 -0.23095296 -0.97228333 471.05620486
-0.03283565 0.97267969 -0.22981740 77.38696713
0.99879726 0.02355737 -0.04300101 36.86598689
Axis 0.12686818 -0.98694672 0.09920002
Axis point 222.17937543 0.00000000 249.34159796
Rotation angle (degrees) 93.05914664
Shift along axis -12.95766466
> hide #!15 models
> select subtract #15
Nothing selected
> show #!14 models
> select add #14
2 models selected
> fitmap #14 inMap #1
Fit map RH-detergent-composite_map-j126_low8.mrc z flip in map
J1551_009_volume_map_sharp.mrc using 225005 points
correlation = 0.7848, correlation about mean = 0.06555, overlap = 5.554e+05
steps = 68, shift = 0.378, angle = 0.231 degrees
Position of RH-detergent-composite_map-j126_low8.mrc z flip (#14) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47526108 0.39871869 -0.78431519 176.36927885
-0.48954236 -0.62086666 -0.61226862 571.04046739
-0.73107810 0.67494296 -0.09988407 263.11747035
Axis 0.82257825 -0.03402057 -0.56763335
Axis point 0.00000000 215.99651892 359.53580790
Rotation angle (degrees) 128.51685438
Shift along axis -23.70384316
> hide #!14 models
> select subtract #14
Nothing selected
> show #!12 models
> select add #12
2 models selected
> fitmap #12 inMap #1
Fit map RH_patfla_J76_006_volume_map_sharp_low8.mrc in map
J1551_009_volume_map_sharp.mrc using 35288 points
correlation = 0.8111, correlation about mean = 0.4405, overlap = 1.156e+04
steps = 52, shift = 0.16, angle = 0.352 degrees
Position of RH_patfla_J76_006_volume_map_sharp_low8.mrc (#12) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98842346 0.15172028 -0.00015448 -25.72536139
0.15172027 -0.98842347 -0.00003354 399.64067529
-0.00015778 0.00000972 -0.99999999 453.95730471
Axis 0.99710149 0.07608298 -0.00007370
Axis point 0.00000000 200.79934453 226.97987333
Rotation angle (degrees) 179.99875710
Shift along axis 4.72160351
> hide #!12 models
> select subtract #12
Nothing selected
> hide #!1 models
> show #!15 models
> show #!14 models
> hide #!15 models
> show #!12 models
> show #!2 models
> volume #14 level 8.842
> volume #2 level 0.2366
> hide #!12 models
> hide #!14 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> select add #2
2 models selected
> fitmap #2 inMap #1
Fit map J1594_005_volume_map_sharp.mrc in map J1551_009_volume_map_sharp.mrc
using 321152 points
correlation = 0.4958, correlation about mean = 0.1729, overlap = 1.37e+04
steps = 40, shift = 0.0253, angle = 0.0191 degrees
Position of J1594_005_volume_map_sharp.mrc (#2) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.86892934 -0.49493562 -0.00072853 519.19497542
-0.49492996 0.86892489 -0.00372335 138.20347203
0.00247585 -0.00287476 -0.99999280 487.32962867
Axis 0.25599722 -0.96667601 0.00170637
Axis point 277.68826926 0.00000000 244.00932361
Rotation angle (degrees) 179.90503668
Shift along axis 0.14605214
> select subtract #2
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.233
> surface dust #2 size 11
> show #!12 models
> volume #12 level 0.7552
> color #12 #b20affff models
> color #12 #b267ffff models
> color #12 #3d2d54ff models
> color #12 #aa7942ff models
> volume #12 level 0.8803
> volume #12 level 0.8916
> volume #12 level 0.8121
> show #!10 models
> volume #10 level 0.908
> surface dust #2 size 11
> surface dust #10 size 22
> surface dust #12 size 22
> hide #!12 models
> volume #10 level 0.8944
> hide #!10 models
> show #!12 models
> volume #12 level 0.7893
> hide #!2 models
> hide #!12 models
> show #!12 models
> volume #12 level 0.8689
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!12 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!12 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!14 models
> volume #13 step 1
> show #!13 models
> hide #!13 models
> hide #!14 models
> show #!14 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!12 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> volume #14 level 8.431
> hide #!14 models
> show #!14 models
> volume #14 level 9.006
> surface dust #1 size 11
> surface dust #14 size 11
> volume #14 level 9.088
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!14 models
> show #!12 models
> select add #14
2 models selected
> transparency sel 50
> select subtract #14
Nothing selected
> hide #!14 models
> show #!14 models
> select add #14
2 models selected
> transparency sel 0
> color #2 #ef6d50ff models
> color #2 #efa450ff models
> color #2 #efa484ff models
> color #2 #ef9484ff models
> color #2 #ef9684ff models
> color #2 #ff9684ff models
> color #2 #f19684ff models
> color #2 #fb9684ff models
> color #2 #fb9884ff models
> color #2 #fb9802ff models
> color #2 #fd9802ff models
> color #2 #ef9802ff models
> color #2 #d59802ff models
> color #2 #d56902ff models
> color #2 #d5695dff models
> select subtract #14
Nothing selected
> color #12 #c18e3fff models
> color #12 #a97b43ff models
> color #12 #bf9140ff models
> color #12 #a87c44ff models
> color #12 #a87c41ff models
> color #12 #a8b041ff models
> color #12 #f5b041ff models
> volume #14 level 9.334
> color #2 #f06e85ff models
> color #2 #d16b5eff models
> select add #2
2 models selected
> ui tool show "Color Actions"
> color sel light coral
> color sel indian red
> select add #14
4 models selected
> color #2.1#14.1 cornflower blue
> undo
> select subtract #2
2 models selected
> color #14.1 forest green
> color #14.1 medium blue
> color #14.1 cornflower blue
> select subtract #14
Nothing selected
> color #2 #e66b5eff models
> color #2 #e66d5eff models
> color #2 #e66d50ff models
> hide #!2 models
> hide #!12 models
> hide #!14 models
> show #!2 models
> show #!15 models
> surface dust #2 size 11
> surface dust #15 size 11
> color #15 #e7ffb2ff models
> color #15 #e7c6b2ff models
> color #15 #e7c661ff models
> volume #15 level 7.408
> hide #!15 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> open /Users/chenxi/Desktop/PDB/7wlu.map
Opened 7wlu.map as #16, grid size 180,180,180, pixel 2.2, shown at level
0.0212, step 1, values float32
> hide #!16 models
> show #!1 models
> hide #!1 models
> show #!16 models
> select add #16
2 models selected
> view matrix models
> #16,-0.97716,0.030484,-0.21033,431.08,0.042349,0.99774,-0.052142,3.9286,0.20826,-0.059858,-0.97624,418.92
> view matrix models
> #16,-0.98042,0.030137,-0.1946,428.24,0.045721,0.99605,-0.076092,9.0352,0.19154,-0.0835,-0.97793,427.43
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.98042,0.030137,-0.1946,432.58,0.045721,0.99605,-0.076092,6.8647,0.19154,-0.0835,-0.97793,474.42
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.70501,-0.69289,-0.15118,516.17,-0.66668,0.72021,-0.1919,229.86,0.24185,-0.034502,-0.9697,452.63
> view matrix models
> #16,-0.70134,-0.69182,-0.17177,519.9,-0.67284,0.72207,-0.16095,223.68,0.23538,0.0026875,-0.9719,446.8
> view matrix models
> #16,-0.76369,-0.64532,-0.018105,487.87,-0.64324,0.76301,-0.063691,187.45,0.054915,-0.036995,-0.99781,496.34
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.76369,-0.64532,-0.018105,487.07,-0.64324,0.76301,-0.063691,186.98,0.054915,-0.036995,-0.99781,478.49
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.97279,-0.23156,-0.0072219,441.29,-0.23098,0.97181,-0.047214,59.344,0.017951,-0.044261,-0.99886,487.5
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.97279,-0.23156,-0.0072219,435.33,-0.23098,0.97181,-0.047214,68.094,0.017951,-0.044261,-0.99886,484.66
> fitmap #16 inMap #2
Fit map 7wlu.map in map J1594_005_volume_map_sharp.mrc using 58259 points
correlation = 0.7026, correlation about mean = 0.08275, overlap = 358.4
steps = 156, shift = 19.9, angle = 5.16 degrees
Position of 7wlu.map (#16) relative to J1594_005_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.97620826 -0.21570018 -0.02215552 83.24376775
0.21572470 0.97645335 -0.00130548 -20.99044940
0.02191543 -0.00350508 0.99975369 9.27155397
Axis -0.00507199 -0.10162193 0.99481016
Axis point 132.70561735 371.54318052 0.00000000
Rotation angle (degrees) 12.52336884
Shift along axis 10.93431421
> select subtract #16
Nothing selected
> volume #16 level 0.02236
> volume #16 level 0.02958
> hide #!2 models
> surface dust #16 size 22
> volume #16 level 0.01915
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #16 level 0.02076
> select add #16
2 models selected
> view matrix models
> #16,-0.95379,-0.30003,0.016052,456,-0.30001,0.95393,0.0034064,84.188,-0.016334,-0.0015667,-0.99987,480.21
> view matrix models
> #16,-0.95379,-0.30003,0.016052,456.76,-0.30001,0.95393,0.0034064,83.025,-0.016334,-0.0015667,-0.99987,480.05
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.95442,-0.29845,0.0005112,460.07,-0.29833,0.95408,0.026945,77.34,-0.0085294,0.025564,-0.99964,472.87
> view matrix models
> #16,-0.9354,-0.35338,-0.012453,470.79,-0.3536,0.93489,0.030643,91.04,0.00081338,0.033067,-0.99945,469.48
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.9354,-0.35338,-0.012453,497.26,-0.3536,0.93489,0.030643,41.143,0.00081338,0.033067,-0.99945,364.4
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.79215,-0.60968,-0.028138,526.75,-0.61031,0.79158,0.030207,120.03,0.003857,0.041101,-0.99915,362.08
> view matrix models
> #16,-0.79503,-0.60064,-0.08464,538.22,-0.60219,0.7983,-0.0086442,125.88,0.07276,0.044097,-0.99637,347.68
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.79503,-0.60064,-0.08464,509.59,-0.60219,0.7983,-0.0086442,179.01,0.07276,0.044097,-0.99637,452.45
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.79553,-0.60326,-0.05663,503.88,-0.60113,0.79752,-0.051097,188.59,0.075988,-0.0066073,-0.99709,462.53
> fitmap #16 inMap #2
Fit map 7wlu.map in map J1594_005_volume_map_sharp.mrc using 60478 points
correlation = 0.9131, correlation about mean = 0.6622, overlap = 615.7
steps = 148, shift = 5.83, angle = 12 degrees
Position of 7wlu.map (#16) relative to J1594_005_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99733712 -0.07292890 -0.00021393 36.91902880
0.07292895 0.99733712 0.00021230 8.01504328
0.00019787 -0.00022733 0.99999996 13.62450437
Axis -0.00301408 -0.00282328 0.99999147
Axis point -91.79729735 510.14253042 0.00000000
Rotation angle (degrees) 4.18226830
Shift along axis 13.49048259
> select subtract #16
Nothing selected
> color #16 #e5bf8fff models
> color #16 #e59d8fff models
> color #16 #299d8fff models
> color #16 #29728fff models
> color #16 #297270ff models
> volume #16 level 0.02196
> volume #2 level 0.2366
> surface dust #2 size 11
> surface dust #16 size 22
> volume #2 level 0.2004
> hide #!16 models
> volume #2 level 0.2149
> volume #2 level 0.2366
> volume #2 level 0.2403
> show #!16 models
> volume #16 level 0.02517
> hide #!2 models
> volume #16 level 0.02356
> show #!2 models
> hide #!16 models
> show #!14 models
> show #!12 models
> color #14 #8a95edff models
> color #14 #8ab0edff models
> color #14 #8ab07cff models
> color #12 #29b041ff models
> color #12 #297241ff models
> color #12 #297270ff models
> hide #!12 models
> hide #!14 models
> show #!16 models
> color #16 #2972baff models
> color #16 #294fbaff models
> color #16 #4a4fbaff models
> color #16 #004fbaff models
> color #16 #015697ff models
> color #16 #0e5697ff models
> color #16 #4f5697ff models
> color #16 #005697ff models
> color #16 #004e89ff models
> color #16 #1a659eff models
> select add #16
2 models selected
> select subtract #16
Nothing selected
> select add #16
2 models selected
> select subtract #16
Nothing selected
> select add #16
2 models selected
> color #16.1 cornflower blue
> select subtract #16
Nothing selected
> select add #16
2 models selected
> select subtract #16
Nothing selected
> select add #16
2 models selected
> fitmap #16 inMap #2
Fit map 7wlu.map in map J1594_005_volume_map_sharp.mrc using 47188 points
correlation = 0.9168, correlation about mean = 0.6526, overlap = 568.8
steps = 36, shift = 0.0289, angle = 0.0141 degrees
Position of 7wlu.map (#16) relative to J1594_005_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99734527 -0.07281723 -0.00025001 36.88319103
0.07281723 0.99734530 -0.00000421 8.07878030
0.00024965 -0.00001401 0.99999997 13.59319224
Axis -0.00006733 -0.00343088 0.99999411
Axis point -92.99486248 509.92024583 0.00000000
Rotation angle (degrees) 4.17584052
Shift along axis 13.56291154
> select subtract #16
Nothing selected
> volume #16 level 0.02036
> volume #2 level 0.2258
[Repeated 1 time(s)]
> volume #16 level 0.02276
> transparency #2.1#16.1 50
> transparency #2.1#16.1 0
> select add #16
2 models selected
> transparency sel 50
> transparency sel 0
> transparency sel 50
> select subtract #16
Nothing selected
> hide #!16 models
> show #!16 models
> transparency #2.1#16.1 0
> color #16 #2995ed80 models
> color #16 #2972ed80 models
> color #16 #29727080 models
> transparency #2.1#16.1 0
> volume #16 level 0.02036
> volume #2 level 0.2258
> volume #16 level 0.02236
> volume #16 level 0.02036
> volume #2 level 0.2258
> hide #!16 models
> show #!12 models
> show #!6 models
> hide #!6 models
> show #!9 models
> hide #!9 models
> show #!14 models
> select add #12
2 models selected
> color #12.1 cornflower blue
> select subtract #12
Nothing selected
> hide #!12 models
> show #!12 models
> color #12 #6295edff models
> color #12 #628dedff models
> color #12 #628aedff models
> color #12 #628dedff models
> color #12 #628debff models
> color #12 #6d8bccff models
> color #12 #6784c1ff models
> color #12 #476fc1ff models
> color #12 #517dc1ff models
> color #12 #4577c1ff models
> color #12 #366ec1ff models
> color #12 #2e6dc1ff models
> color #12 #276fc1ff models
> color #12 #2976ccff models
> color #12 #2364aeff models
> color #12 #256ab8ff models
> color #12 #3d70b8ff models
> color #12 #4b73b8ff models
> hide #!12 models
> hide #!14 models
> hide #!2 models
> show #!8 models
> show #!9 models
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> transparency sel 50
> transparency sel 0
> select subtract #8
Nothing selected
> select add #9
2 models selected
> ui tool show "Color Actions"
> color sel gray
> color sel dark gray
> select subtract #9
Nothing selected
> select add #8
2 models selected
> ui tool show "Color Actions"
> color sel thistle
> color sel medium purple
> color sel plum
[Repeated 1 time(s)]
> color sel thistle
> color sel light pink
> color sel light coral
> color sel dark green
> color sel pale violet red
[Repeated 1 time(s)]
> color sel pink
> color sel light pink
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> color #8 #e0b6bcff models
> color #8 #e09abbff models
> color #8 #e08eb6ff models
> color #8 #e094b7ff models
> color #8 #e099bcff models
> color #8 #e093b9ff models
> color #8 #e08fb9ff models
> color #8 #e09db8ff models
> color #8 #e097b2ff models
> color #8 #e08faeff models
> color #8 #e090a3ff models
> color #8 #e099aeff models
> color #8 #e09aabff models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> show #!14 models
> show #!12 models
> color #12 #c096b5ff models
> color #12 #c08fadff models
> color #12 #c086aeff models
> color #12 #c09eafff models
> color #12 #c09fbdff models
> color #12 #c09eb7ff models
> color #12 #c0a0afff models
[Repeated 1 time(s)]
> color #12 #ffa0afff models
> color #12 #ff92afff models
> color #12 #ff9bafff models
> color #12 #ff9bc1ff models
> color #12 #ff9bbcff models
> color #2 #ce7ddfff models
> color #2 #b782dfff models
> color #2 #a47fdfff models
> color #2 #a37fdfff models
> color #2 #977fdfff models
> color #2 #976edfff models
> color #2 #a693dfff models
> color #2 #ac9adfff models
> color #2 #9b90dfff models
> color #2 #a19edfff models
> color #2 #8885dfff models
> color #2 #9292dfff models
> color #2 #968fdfff models
> color #2 #9b9bdfff models
> color #2 #9792dfff models
> color #14 #8da7bbff models
> color #14 #879dbbff models
> color #14 #92aabbff models
> color #14 #b6d3e9ff models
> color #14 #6daae9ff models
> color #14 #6daaffff models
> color #14 #67aaffff models
> color #14 #67b2ffff models
> color #14 #94d7ffff models
> color #14 #9fdaffff models
> color #14 #99d3ffff models
> color #14 #85b7deff models
> color #14 #84b6dcff models
> hide #!12 models
> hide #!14 models
> show #!16 models
> color #16 #7f825bff models
> color #16 #827e5fff models
> color #16 #dcd4a1ff models
> color #16 #dccda1ff models
> color #16 #dccd83ff models
> color #16 #eccd83ff models
> color #16 #e2cd83ff models
> color #16 #e2e883ff models
> color #16 #e2c383ff models
> color #16 #e2c983ff models
> color #16 #e2c283ff models
> color #16 #e2c274ff models
> color #16 #e2c27dff models
> color #16 #efcd86ff models
> color #16 #e8c782ff models
> color #16 #e7c782ff models
> color #16 #e7c682ff models
> color #16 #e7c66bff models
> hide #!16 models
> show #!15 models
> color #15 #b7e7b2ff models
> color #15 #c6e7b5ff models
> color #15 #c1e7a2ff models
> color #15 #bee79aff models
> color #15 #c0e794ff models
> color #15 #ade792ff models
> color #15 #adf692ff models
> color #15 #adf69dff models
> color #15 #a4ec98ff models
> color #15 #a1ec93ff models
> color #15 #98ec9fff models
> color #15 #baeca6ff models
> color #15 #ddeca0ff models
> color #15 #aeec93ff models
> color #15 #8aec93ff models
> color #15 #8ab093ff models
> color #15 #8ab07cff models
> color #15 #89b07cff models
> color #15 #92bc85ff models
> color #15 #91ba83ff models
> hide #!15 models
> show #!9 models
> hide #!2 models
> show #!8 models
> color #8 #dea191ff models
> color #8 #de8792ff models
> color #8 #de6c72ff models
> color #8 #de4e66ff models
> color #8 #de7064ff models
> color #8 #cf695dff models
> color #8 #ce685cff models
> select add #8
2 models selected
> ui tool show "Color Actions"
> color sel light coral
> color sel indian red
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel burly wood
> color sel tan
> ui tool show "Color Actions"
> color sel peach puff
> color sel sandy brown
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel sandy brown
> color sel orange
> color sel sandy brown
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> color #2 #9780dfff models
> color #2 #8f80dfff models
> color #2 #9080dfff models
> color #2 #9079dfff models
> show #!12 models
> show #!14 models
> color #14 #8eb6dcff models
> color #14 #8cb6dcff models
> color #14 #8cb6ffff models
> color #2 #2979dfff models
> color #2 #2972dfff models
> color #2 #297270ff models
> color #12 #8a9bbcff models
> color #12 #8ab0bcff models
> color #12 #8ab07cff models
> color #14 #ffb6ffff models
> color #14 #ffa3ffff models
> color #14 #ffa3deff models
> color #14 #ffa3daff models
> color #14 #ff99daff models
> color #14 #ff9adaff models
> color #14 #ff9ad2ff models
> color #14 #ff9ad8ff models
[Repeated 1 time(s)]
> color #12 #8ab0ffff models
> color #12 #64b0ffff models
> color #12 #7ab0ffff models
> color #12 #7aa4ffff models
> color #12 #7aa400ff models
> color #12 #7aa4ffff models
> select add #12
2 models selected
> ui tool show "Color Actions"
> color sel goldenrod
> color sel light salmon
> color sel wheat
> color sel black
> color sel ivory
> color sel light gray
> color sel magenta
> color sel cornflower blue
> hide #!12 models
> show #!12 models
> select subtract #12
Nothing selected
> color #12 #8a95edff models
> color #12 #8ab0edff models
> color #12 #8ab07cff models
> hide #!12 models
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #!15 models
> color #15 #e7ba83ff models
> color #15 #e7c683ff models
> color #15 #e7c66bff models
> ui windowfill toggle
[Repeated 3 time(s)]
> open /Users/chenxi/Desktop/RH-figure/7wlu_low8.mrc
Opened 7wlu_low8.mrc as #17, grid size 180,180,180, pixel 2.2, shown at level
0.0205, step 1, values float32
> ui windowfill toggle
[Repeated 7 time(s)]
> save /Users/chenxi/Desktop/map-align.cxs includeMaps true
——— End of log from Tue Aug 19 20:49:45 2025 ———
opened ChimeraX session
> select add #17
2 models selected
> hide #!15 models
> hide #!2 models
> show #!1 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.55324,-0.79199,-0.25822,519.1,-0.72879,0.61032,-0.31044,290.43,0.40346,0.016443,-0.91485,355.9
> view matrix models
> #17,-0.67268,-0.73956,-0.023706,477.56,-0.72576,0.65321,0.21585,161.07,-0.14414,0.1624,-0.97614,443.96
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.67268,-0.73956,-0.023706,511.36,-0.72576,0.65321,0.21585,187.55,-0.14414,0.1624,-0.97614,447.94
> view matrix models
> #17,-0.67268,-0.73956,-0.023706,503.49,-0.72576,0.65321,0.21585,182.43,-0.14414,0.1624,-0.97614,447.3
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.91889,-0.39126,-0.050593,484.31,-0.39341,0.89915,0.1917,73.586,-0.029515,0.19606,-0.98015,419.38
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.91889,-0.39126,-0.050593,480.83,-0.39341,0.89915,0.1917,76.68,-0.029515,0.19606,-0.98015,432.31
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.92404,-0.37829,0.055172,455.03,-0.37838,0.9256,0.0091999,109.9,-0.054548,-0.012375,-0.99843,484.48
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.92404,-0.37829,0.055172,457.85,-0.37838,0.9256,0.0091999,105.01,-0.054548,-0.012375,-0.99843,484.06
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.92492,-0.37151,0.080688,450.8,-0.37281,0.92791,-0.0012138,105.84,-0.07442,-0.031204,-0.99674,491.36
> view matrix models
> #17,-0.91653,-0.39109,0.083724,452.57,-0.3929,0.91956,-0.0056292,112.41,-0.074788,-0.038054,-0.99647,492.79
> view matrix models
> #17,-0.92713,-0.36685,0.076504,451.21,-0.37325,0.9222,-0.10114,129.87,-0.033451,-0.12232,-0.99193,501.35
> view matrix models
> #17,-0.91136,-0.40249,0.086191,453.39,-0.41021,0.90541,-0.10935,142.27,-0.034026,-0.13501,-0.99026,503.72
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.91136,-0.40249,0.086191,464.49,-0.41021,0.90541,-0.10935,140.31,-0.034026,-0.13501,-0.99026,506.66
> fitmap #17 inMap #1
Fit map 7wlu_low8.mrc in map J1551_009_volume_map_sharp.mrc using 58286 points
correlation = 0.5206, correlation about mean = 0.07947, overlap = 234.5
steps = 124, shift = 6.96, angle = 8.19 degrees
Position of 7wlu_low8.mrc (#17) relative to J1551_009_volume_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.90879794 -0.41722572 -0.00299969 482.30258602
-0.41723025 0.90880020 0.00105719 122.16710965
0.00228503 0.00221234 -0.99999494 470.25976856
Axis 0.21353991 -0.97693398 -0.00083676
Axis point 254.17755921 0.00000000 235.41386860
Rotation angle (degrees) 179.84502924
Shift along axis -16.75184491
> hide #!1 models
> select subtract #17
Nothing selected
> show #!2 models
> color #17 #e6bfe5ff models
> color #17 #e66de5ff models
> color #17 #e66d50ff models
> volume #17 level 0.01887
> hide #!17 models
> show #!17 models
> volume #17 level 0.01942
> volume #17 level 0.02053
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!15 models
> color #15 #e7c678ff models
> color #15 #ffc678ff models
> color #15 #ffbb78ff models
> color #15 #ffb478ff models
> color #15 #ffb476ff models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select add #15
2 models selected
> fitmap #15 inMap #1
Fit map 8IXO-35800_low8.mrc z flip in map J1551_009_volume_map_sharp.mrc using
219548 points
correlation = 0.6091, correlation about mean = 0.1831, overlap = 3.724e+05
steps = 48, shift = 0.261, angle = 0.423 degrees
Position of 8IXO-35800_low8.mrc z flip (#15) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.03100645 -0.22764736 -0.97324985 469.17376248
-0.02906814 0.97351155 -0.22678250 75.70350153
0.99909641 0.02125885 -0.03680242 36.11855812
Axis 0.12415875 -0.98727109 0.09940015
Axis point 221.27866998 0.00000000 249.30431051
Rotation angle (degrees) 92.70242109
Shift along axis -12.89766037
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select subtract #15
Nothing selected
> hide #!15 models
> show #!1 models
> select add #2
2 models selected
> fitmap #2 inMap #1
Fit map J1594_005_volume_map_sharp.mrc in map J1551_009_volume_map_sharp.mrc
using 371209 points
correlation = 0.4989, correlation about mean = 0.176, overlap = 1.453e+04
steps = 60, shift = 0.216, angle = 0.181 degrees
Position of J1594_005_volume_map_sharp.mrc (#2) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.86930745 -0.49426828 -0.00185038 519.35711826
-0.49426754 0.86930940 -0.00086854 137.40871482
0.00203785 0.00015955 -0.99999791 486.55572328
Axis 0.25562715 -0.96677543 0.00018332
Axis point 277.59181100 0.00000000 243.56095888
Rotation angle (degrees) 179.88478228
Shift along axis 0.00760557
> select subtract #2
Nothing selected
> hide #!2 models
> show #!15 models
> select add #15
2 models selected
> fitmap #15 inMap #1
Fit map 8IXO-35800_low8.mrc z flip in map J1551_009_volume_map_sharp.mrc using
219548 points
correlation = 0.6091, correlation about mean = 0.183, overlap = 3.724e+05
steps = 44, shift = 0.035, angle = 0.0524 degrees
Position of 8IXO-35800_low8.mrc z flip (#15) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.03037433 -0.22749359 -0.97330574 468.99123448
-0.02842292 0.97355785 -0.22666552 75.51236668
0.99913439 0.02077938 -0.03603720 36.03578776
Axis 0.12385600 -0.98728466 0.09964278
Axis point 221.19055389 0.00000000 249.33244791
Rotation angle (degrees) 92.66101844
Shift along axis -12.87411568
> hide #!1 models
> show #!2 models
> select subtract #15
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!15 models
> show #!8 models
> hide #!2 models
> show #!14 models
> show #!1 models
> hide #!14 models
> select add #8
2 models selected
> fitmap #8 inMap #1
Fit map 切整个blade-postprocess_masked_job217_blade.mrc z flip in map
J1551_009_volume_map_sharp.mrc using 33254 points
correlation = 0.8168, correlation about mean = 0.5313, overlap = 449.2
steps = 24, shift = 0.00657, angle = 0.00257 degrees
Position of 切整个blade-postprocess_masked_job217_blade.mrc z flip (#8) relative
to J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.96324712 -0.26861680 -0.00009960 73.16903162
0.26861679 0.96324712 -0.00006461 -40.08562970
0.00011330 0.00003548 0.99999999 11.00411697
Axis 0.00018632 -0.00039630 0.99999990
Axis point 183.05499532 247.33813084 0.00000000
Rotation angle (degrees) 15.58197621
Shift along axis 11.03363490
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> fitmap #1 inMap #8
Fit map J1551_009_volume_map_sharp.mrc in map 切整个blade-
postprocess_masked_job217_blade.mrc z flip using 172515 points
correlation = 0.8611, correlation about mean = 0.488, overlap = 2958
steps = 48, shift = 0.0863, angle = 0.154 degrees
Position of J1551_009_volume_map_sharp.mrc (#1) relative to 切整个blade-
postprocess_masked_job217_blade.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.96252883 0.27117934 -0.00012171 -60.03153010
-0.27117937 0.96252880 -0.00023652 59.07880934
0.00005301 0.00026066 0.99999996 -11.18188271
Axis 0.00091671 -0.00032215 -0.99999953
Axis point 183.76914398 246.80256451 0.00000000
Rotation angle (degrees) 15.73446504
Shift along axis 11.10781356
> hide #!1 models
> show #!9 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!5 models
> hide #!5 models
> select add #4
2 models selected
> hide #!5 target m
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> select subtract #4
Nothing selected
> select add #8
2 models selected
> transparency sel 50
> select subtract #8
Nothing selected
> transparency #8.1#9.1 0
> color #8 #f4a4f9ff models
> color #8 #8a6b8fff models
> color #8 #99779fff models
> color #8 #7b6c9fff models
> color #8 #a691d6ff models
> color #8 #9270d6ff models
> color #8 #906cd6ff models
> color #8 #9a6fd6ff models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> show #!12 models
> show #!14 models
> color #12 #8ca8bbff models
> color #12 #5999bbff models
> color #12 #4761bbff models
> color #12 #afbb89ff models
> color #12 #b6bb7dff models
> color #12 #9bbb82ff models
> show #!15 models
> hide #!15 models
> color #12 #ffb476ff models
> hide #!12 models
> hide #!14 models
> show #!12 models
> show #!14 models
> volume #14 level 9.334
> hide #!12 models
> hide #!14 models
> show #!15 models
> color #15 #8ab476ff models
> color #15 #8ab076ff models
> color #15 #8ab07cff models
> color #15 #a2bd95ff models
> hide #!15 models
> show #!15 models
> hide #!2 models
> show #!2 models
> hide #!15 models
> show #!17 models
> surface dust #2 size 11
> surface dust #17 size 22
> show #!15 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!5 models
> hide #!5 models
> show #!16 models
> hide #!16 models
> show #!12 models
> hide #!12 models
> save /Users/chenxi/Desktop/map-align.cxs
——— End of log from Wed Aug 20 01:50:05 2025 ———
opened ChimeraX session
> view orient
[Repeated 2 time(s)]
> turn x, 90
Expected an axis vector or a keyword
> turn x 90
> turn y 30
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!17 models
> color #2 #7f7182ff models
> color #2 #d9c2dfff models
> color #2 #d2bcd8ff models
> color #2 #d5a4d8ff models
> color #2 #b893d8ff models
> color #2 #bb9fd8ff models
> color #2 #b191d8ff models
> color #2 #b39bd8ff models
> lighting soft
> lighting simple
> transparency #2.1 50
> volume #!2 style image
> volume #!2 style surface
> transparency #2.1 0
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> close #7
> close #6
> close #3
> close #10
> close #13
> show #!5 models
> hide #!5 models
> close #5
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> view orient
[Repeated 1 time(s)]
> turn x 90
> turn y 90
> turn y 10
[Repeated 20 time(s)]
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!17 models
> color #17 #dfd79bff models
> color #17 #d6df93ff models
> color #17 #dfd59dff models
> color #17 #dfc697ff models
> color #17 #ecd2a1ff models
> color #17 #ece3b0ff models
> color #17 #ece291ff models
> color #17 #eccb7bff models
> color #17 #eccd86ff models
> color #17 #eccd91ff models
> color #17 #ece6b4ff models
> color #17 #ece2b6ff models
> color #17 #ecdbaaff models
> color #17 #ecd29fff models
> color #17 #ecd88cff models
> color #17 #ecd376ff models
> color #17 #eccd8aff models
> color #17 #ecd698ff models
> color #2 #badcb8ff models
> color #2 #b1dca1ff models
> color #2 #addc91ff models
> color #2 #a8dfa1ff models
> color #2 #7ca477ff models
> color #2 #87b381ff models
> color #2 #9ab386ff models
> color #2 #98b393ff models
> color #2 #84b382ff models
> color #2 #96b389ff models
> color #2 #9fbd92ff models
> color #17 #edb777ff models
> color #17 #eda140ff models
> color #17 #b27930ff models
> color #17 #b29785ff models
> color #17 #b28f5fff models
> color #17 #b26b2fff models
> color #17 #ff9944ff models
> color #17 #ffa667ff models
> color #17 #ffa73cff models
> color #17 #ff9176ff models
> color #17 #ff9157ff models
> color #17 #e69157ff models
> color #17 #e66d57ff models
> color #17 #e66d50ff models
> undo
[Repeated 9 time(s)]
> color #2 #e6ffd7ff models
> color #2 #eac3ffff models
> color #2 #d8c4ffff models
> color #2 #bfade1ff models
> color #2 #c8aee1ff models
> color #2 #e2c5ffff models
> color #2 #bb9cffff models
> color #2 #b6a8ffff models
> color #2 #ba98ffff models
> color #2 #c3b5ffff models
> color #17 #dfdfa8ff models
> color #17 #dfcfa0ff models
> color #17 #dfd08dff models
> color #17 #dfbf8cff models
> color #17 #dfc997ff models
> color #17 #dbdf8eff models
> color #17 #c9df8fff models
> color #17 #dadf8aff models
> color #17 #dfd8a8ff models
> color #17 #dfc9abff models
> color #17 #dfcf8bff models
> color #17 #dfd382ff models
> color #17 #fff195ff models
> color #17 #fcee93ff models
> color #17 #fcee80ff models
> color #17 #ffee80ff models
> color #17 #ffe780ff models
> color #17 #ffe280ff models
> color #2 #8db5ffff models
> color #2 #a2b5ffff models
> color #2 #bbb5ffff models
> color #2 #bfb5ffff models
> color #2 #cab5ffff models
> color #2 #dab5ffff models
> color #2 #cdb5ffff models
> color #2 #b6dafbff models
> color #2 #94e8fbff models
> color #2 #9cd6fbff models
> color #2 #98cafbff models
> color #2 #9dc0fbff models
> color #2 #a5befbff models
> color #2 #a5beffff models
> color #2 #96beffff models
> color #2 #9bbeffff models
> color #2 #99beffff models
> save /Users/chenxi/Desktop/RH-figure/rhf+7wlu.png width 704 height 425
> supersample 3
> color #17 #ffca80ff models
> color #2 #a1beffff models
> color #2 #b6ceffff models
[Repeated 1 time(s)]
> color #2 #9aaed8ff models
> color #2 #85a6d8ff models
> color #2 #90b3eaff models
> save /Users/chenxi/Desktop/RH-figure/rhf+7wlu.png width 704 height 425
> supersample 3
> open
> "/Users/chenxi/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/1a46e1e28e60cf7334b260325fd7789f/Message/MessageTemp/b0b8b2e961018fad0afb51d977868ae1/File/P1SE_flattened_apply_ncs_105.pdb"
Summary of feedback from opening
/Users/chenxi/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
Support/com.tencent.xinWeChat/2.0b4.0.9/1a46e1e28e60cf7334b260325fd7789f/Message/MessageTemp/b0b8b2e961018fad0afb51d977868ae1/File/P1SE_flattened_apply_ncs_105.pdb
---
warnings | Ignored bad PDB record found on line 10509
Ignored bad PDB record found on line 10614
Ignored bad PDB record found on line 10723
Ignored bad PDB record found on line 10775
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
10501 messages similar to the above omitted
Ignored bad PDB record found on line 21283
Duplicate atom serial number found: 10507
Duplicate atom serial number found: 10508
Duplicate atom serial number found: 10509
Duplicate atom serial number found: 10510
Duplicate atom serial number found: 10511
99 messages similar to the above omitted
Ignored bad PDB record found on line 21388
Duplicate atom serial number found: 10611
Duplicate atom serial number found: 10612
Duplicate atom serial number found: 10613
Duplicate atom serial number found: 10614
Duplicate atom serial number found: 10615
103 messages similar to the above omitted
Ignored bad PDB record found on line 21497
Duplicate atom serial number found: 10719
Duplicate atom serial number found: 10720
Duplicate atom serial number found: 10721
Duplicate atom serial number found: 10722
Duplicate atom serial number found: 10723
46 messages similar to the above omitted
Ignored bad PDB record found on line 21549
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
10501 messages similar to the above omitted
Ignored bad PDB record found on line 32057
Duplicate atom serial number found: 10507
Duplicate atom serial number found: 10508
Duplicate atom serial number found: 10509
Duplicate atom serial number found: 10510
Duplicate atom serial number found: 10511
99 messages similar to the above omitted
Ignored bad PDB record found on line 32162
Duplicate atom serial number found: 10611
Duplicate atom serial number found: 10612
Duplicate atom serial number found: 10613
Duplicate atom serial number found: 10614
Duplicate atom serial number found: 10615
103 messages similar to the above omitted
Ignored bad PDB record found on line 32271
Duplicate atom serial number found: 10719
Duplicate atom serial number found: 10720
Duplicate atom serial number found: 10721
Duplicate atom serial number found: 10722
Duplicate atom serial number found: 10723
46 messages similar to the above omitted
Ignored bad PDB record found on line 32323
Ignored bad PDB record found on line 32324
Chain information for P1SE_flattened_apply_ncs_105.pdb #3
---
Chain | Description
A B F | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> close #3
> hide #!17 models
> show #!15 models
> color #15 #e3fad5ff models
> color #15 #dcf2cfff models
> color #15 #f2cbebff models
> color #15 #f2c0d8ff models
> color #15 #f2b0c6ff models
> color #15 #f2a5bbff models
> color #15 #f2aabfff models
> color #15 #f2a7bcff models
> save /Users/chenxi/Desktop/RH-figure/rhf+8ixo.png width 704 height 425
> supersample 3
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!14 models
> show #!12 models
> color #14 #d0d4f5ff models
> color #14 #c7aef5ff models
> color #14 #beadf5ff models
> color #14 #a599f5ff models
> color #14 #b299f5ff models
> color #14 #b499f5ff models
> color #14 #b49ff5ff models
> color #14 #c2acf5ff models
> color #14 #baa5f5ff models
> color #14 #baa7f5ff models
> color #14 #bba7f5ff models
> color #14 #c2aeffff models
> color #14 #baa6f4ff models
> color #14 #beaaf9ff models
> color #14 #ba9df9ff models
> color #14 #aba3f9ff models
> color #14 #b3a0f9ff models
> color #14 #b3a0ffff models
> color #14 #b3a4ffff models
> color #14 #b3a5ffff models
> color #14 #c5a5ffff models
> color #14 #c4a5ffff models
> color #14 #c5a5ffff models
> color #12 #c1f7bfff models
> color #12 #c0f79dff models
> color #12 #b6f77fff models
> color #12 #c6f778ff models
> color #12 #c4f7aaff models
> color #12 #d4f7adff models
> color #12 #c1f7abff models
> color #12 #c6f7b2ff models
> color #12 #beeeabff models
> color #12 #beeea1ff models
> color #12 #beffa1ff models
> color #12 #abffa1ff models
> color #12 #c9ff9fff models
> color #12 #b1e08cff models
> color #12 #b8e07cff models
> color #12 #abe079ff models
> color #12 #bbe07fff models
> color #12 #a4c56fff models
> color #12 #8ab07cff models
> color #12 #92bc84ff models
> color #12 #94be86ff models
> color #12 #94cb86ff models
> color #12 #94c986ff models
> color #12 #94cb86ff models
> save /Users/chenxi/Desktop/RH-figure/3RH.png width 704 height 425
> supersample 3
> hide #!2 models
> hide #!12 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!8 models
> show #!9 models
> color #8 #d8b2bdff models
> color #8 #d891b4ff models
> color #8 #d88fa3ff models
> color #8 #d899a0ff models
> color #8 #d87e88ff models
> color #8 #d87477ff models
> color #8 #d88b89ff models
> color #8 #d88185ff models
> show #!15 models
> color #8 #d86c65ff models
> color #8 #d88b77ff models
> color #8 #d89c75ff models
> color #8 #d8ab85ff models
> color #8 #d8906aff models
> color #8 #d8a685ff models
> color #8 #d89a75ff models
> color #8 #d89986ff models
> color #8 #d8ac89ff models
> color #8 #d89d6dff models
> color #8 #d89966ff models
> color #8 #d8975eff models
> hide #!15 models
> color #9 #bec0c0ff models
> save /Users/chenxi/Desktop/RH-figure/5z10+gsmt.png width 704 height 425
> supersample 3
> save "/Users/chenxi/Desktop/RH-figure/map align.cxs" includeMaps true
——— End of log from Wed Aug 20 15:25:24 2025 ———
opened ChimeraX session
> hide #!8 models
> hide #!9 models
> volume #2 color #90b3f4
> volume #2 color #90b3f5
> volume #2 color #90b3ff
> open
> /Users/chenxi/Desktop/0817_lipf/rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb
Chain information for rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb #3
---
Chain | Description
A B C | No description available
> open
> /Users/chenxi/Desktop/0808rhlip_all/rhlipc0808/rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb
Chain information for
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #5
---
Chain | Description
A B C | No description available
> hide #!5 models
> show #!5 models
> select add #5
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,2.7703,0,1,0,-4.7983,0,0,1,-15.503
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.60291,-0.26085,-0.75396,335.57,-0.1176,0.90566,-0.40737,141.98,0.78909,0.33427,0.51536,-157.45
> view matrix models
> #5,-0.59739,-0.79887,-0.070211,570.94,-0.79784,0.6009,-0.048698,282.29,0.081093,0.026925,-0.99634,441.41
> view matrix models
> #5,-0.63408,-0.75576,-0.16362,592.54,-0.75027,0.65251,-0.10643,273.65,0.1872,0.055273,-0.98077,406.51
> view matrix models
> #5,-0.84852,-0.52174,-0.088289,572.81,-0.51445,0.85244,-0.093231,170.94,0.1239,-0.033689,-0.99172,443.68
> view matrix models
> #5,-0.8671,-0.48989,-0.090265,570.59,-0.4945,0.86837,0.037396,131.21,0.060064,0.077062,-0.99522,434.97
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.8671,-0.48989,-0.090265,538.14,-0.4945,0.86837,0.037396,132.37,0.060064,0.077062,-0.99522,441.72
> view matrix models
> #5,-0.8671,-0.48989,-0.090265,541.93,-0.4945,0.86837,0.037396,131.23,0.060064,0.077062,-0.99522,458.04
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.87661,-0.47961,-0.039061,529.52,-0.48119,0.87313,0.078136,117.23,-0.0033699,0.08729,-0.99618,470.88
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.87661,-0.47961,-0.039061,527.74,-0.48119,0.87313,0.078136,113.99,-0.0033699,0.08729,-0.99618,470.18
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.84232,0.23173,-0.48663,470.26,-0.18138,-0.97207,-0.14893,507.02,-0.50755,-0.03718,0.86082,167.65
> view matrix models
> #5,-0.95113,0.2905,0.10473,340.01,-0.28919,-0.95687,0.027766,486.27,0.10828,-0.0038797,0.99411,-16.222
> view matrix models
> #5,-0.92912,0.34957,0.12059,317.95,-0.35308,-0.93555,-0.008427,505.26,0.10987,-0.050407,0.99267,-5.9455
> view matrix models
> #5,-0.55405,0.8286,0.080286,133.73,-0.83237,-0.55296,-0.037291,539.86,0.013496,-0.087489,0.99607,24.028
> view matrix models
> #5,-0.58072,0.81045,0.077059,144.78,-0.81408,-0.57873,-0.048339,543.94,0.0054207,-0.090804,0.99585,26.707
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.58072,0.81045,0.077059,145.84,-0.81408,-0.57873,-0.048339,542.45,0.0054207,-0.090804,0.99585,18.423
> fitmap #5 inMap #1
Fit molecule rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb (#5)
to map J1551_009_volume_map_sharp.mrc (#1) using 37605 atoms
average map value = 0.3707, steps = 124
shifted from previous position = 7.13
rotated from previous position = 7.59 degrees
atoms outside contour = 16109, contour level = 0.28714
Position of rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb (#5)
relative to J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.50048314 0.86574628 -0.00004153 139.38438215
-0.86574629 -0.50048314 -0.00007205 519.61233972
-0.00008314 -0.00000010 1.00000000 0.04617148
Axis 0.00004156 0.00002403 -1.00000000
Axis point 219.59472693 219.59528480 0.00000000
Rotation angle (degrees) 120.03196947
Shift along axis -0.02789161
> select subtract #5
Nothing selected
> hide #!5 models
> show #!3 models
> select add #3
34275 atoms, 35055 bonds, 45 pseudobonds, 4446 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91107,0.13103,0.39087,-106.31,0.055967,-0.97868,0.19762,421.94,0.40843,-0.15817,-0.89898,405.21
> view matrix models
> #3,0.87865,0.12238,0.46152,-114.16,0.11142,-0.99246,0.051049,448.48,0.46429,0.0065657,-0.88566,350.01
> view matrix models
> #3,0.84905,0.29226,0.44012,-144.02,0.26271,-0.95631,0.12824,388.83,0.45837,0.0067467,-0.88874,351.96
> view matrix models
> #3,0.92855,0.33136,0.1673,-105.3,0.33475,-0.94227,0.0083507,398.67,0.16041,0.048251,-0.98587,428.9
> view matrix models
> #3,0.9243,-0.34666,0.15967,62.322,-0.33365,-0.93705,-0.10302,567.14,0.18533,0.041947,-0.98178,424.12
> view matrix models
> #3,0.92497,-0.33688,0.1759,55.919,-0.3079,-0.9356,-0.17276,577.96,0.22277,0.10563,-0.96913,397.59
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.92497,-0.33688,0.1759,39.83,-0.3079,-0.9356,-0.17276,536.2,0.22277,0.10563,-0.96913,399
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91543,-0.34283,0.21086,34.96,-0.32699,-0.93895,-0.10704,525.38,0.23468,0.029044,-0.97164,415.68
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91543,-0.34283,0.21086,35.742,-0.32699,-0.93895,-0.10704,525.8,0.23468,0.029044,-0.97164,425.91
> fitmap #3 inMap #1
Fit molecule rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb (#3) to map
J1551_009_volume_map_sharp.mrc (#1) using 34275 atoms
average map value = 0.1362, steps = 312
shifted from previous position = 26.8
rotated from previous position = 14.2 degrees
atoms outside contour = 29363, contour level = 0.28714
Position of rhlipf0814_ncs70_realspace_refined_072-coot-0.pdb (#3) relative to
J1551_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88213522 -0.46715239 0.06005079 110.36357636
-0.46906846 -0.88287861 0.02236374 510.33972585
0.04257028 -0.04789577 -0.99794477 465.36784893
Axis -0.97007643 0.24135417 -0.02645531
Axis point 0.00000000 273.24450454 226.42323907
Rotation angle (degrees) 177.92467203
Shift along axis 3.80006705
> hide #!1 models
> show #!5 models
> select subtract #3
Nothing selected
> cartoon style #3,5 modeHelix tube sides 20
[Repeated 1 time(s)]
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!5 models
> close #5
> show #!3 models
> close #3
> save "/Users/chenxi/Desktop/RH-figure/map align.cxs" includeMaps true
——— End of log from Thu Aug 21 16:31:39 2025 ———
opened ChimeraX session
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!12 models
> show #!14 models
> hide #!12 models
> volume #14 level 5.968
> volume #14 level 4.407
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting soft
> volume #!14 hide
> volume show
> volume hide
> show #!14 models
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting soft
> lighting full
> lighting simple
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> volume #14 level 6.46
> volume #14 level 7.856
> hide #!14 models
> show #!8 models
> select add #8
2 models selected
No visible atoms or bonds selected
> select subtract #8
Nothing selected
> hide #!8 models
> show #!14 models
> view orient
> turn x 90
> volume #14 level 4.736
> turn y -40
> turn y 5
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #!4 models
> hide #!4 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!9 models
> turn y -20
> hide #!9 models
> show #!14 models
> volume #14 level 5.311
> ui tool show "Side View"
> save /Users/chenxi/Desktop/RH-figure/map/rhdc.png width 2000 height 1219
> supersample 3 transparentBackground true
> hide #!14 models
> show #!14 models
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save /Users/chenxi/Desktop/RH-figure/map/rhdc.png width 2000 height 1219
> supersample 3 transparentBackground true
> hide #!14 models
> show #!12 models
> volume #12 level 0.9712
> volume #12 level 0.9598
> save /Users/chenxi/Desktop/RH-figure/map/rhdpc.png width 2000 height 1219
> supersample 3 transparentBackground true
> hide #!12 models
> show #!1 models
> open /Users/chenxi/Desktop/RH_map-model/P1R2482H-part-
> flat-20250823/J76_006_volume_map_sharp.mrc
Opened J76_006_volume_map_sharp.mrc as #3, grid size 196,196,196, pixel 2.2,
shown at level 0.636, step 1, values float32
> hide #!1 models
> rename #3 RHpartf
> open /Users/chenxi/Desktop/RH_map-model/mP1-RH-detergent/RH-full-length/RH-
> detergent-composite_map-j126.ccp4
Opened RH-detergent-composite_map-j126.ccp4 as #5, grid size 400,400,400,
pixel 1.1, shown at level 5.1, step 2, values float32
> hide #!3 models
> rename #5 RHdc
> show #!8 models
> hide #!8 models
> close #8
> color #5 #c5ffb2ff models
> color #5 #c5a5b2ff models
> color #5 #c5a5ffff models
> open /Users/chenxi/Desktop/RH_map-model/mP1-RH-detergent/RH-full-
> length/RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb
Chain information for
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb #6
---
Chain | Description
A B C | No description available
> select add #6
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected
> hide (#!6 & sel) target a
> show sel cartoons
> select subtract #6
Nothing selected
> volume zone #5 nearAtoms #6 range 6.59
> volume #5 step 1
> volume #!5 region all imageMode "full region"
> volume unzone #!5
> mousemode rightMode "crop volume"
> volume #!5 style surface
> volume #5 change image level -0.2509,0 level 5.091,0.8 level 45.58,1
> volume #5 level 5.833
> volume #5 level 6.939
> color #5 near #6 distance 2.5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #5 near #6 distance 2.5
> volume #5 level 11
> hide #!6 models
> color zone #5 near #6 distance 3.5
> color zone #5 near #6 distance 5.5
> color zone #5 near #6 distance 7.5
> color zone #5 near #6 distance 8.5
> color zone #5 near #6 distance 12.5
> color zone #5 near #6 distance 20.5
> surface dust #5 size 11
> volume #5 level 12.23
> volume #5 level 8.169
> color zone #5 near #6 distance 25.5
> color zone #5 near #6 distance 35.5
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> volume #5 level 6.816
> volume #5 level 7.308
> volume #5 level 8.046
> view orient
> show #!1 models
> view orient
> hide #!5 models
> show #!5 models
> hide #!1 models
> view orient
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> color zone #5 near #6 distance 33.5
> volume #5 level 8.538
> surface dust #5 size 11
> volume #5 level 8.784
> volume #5 level 8.169
> color zone #5 near #6 distance 35.5
> show #!1 models
> hide #!1 models
> show #!1 models
> rename #1 rhlc
> show #!2 models
> hide #!2 models
> select add #5
3 models selected
> volume #1 region 0,0,0,399,399,399
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.91399,0.16264,0.37173,-95.529,0.18494,-0.98243,-0.024896,347.64,0.36115,0.091503,-0.92801,333.63
> view matrix models
> #5,0.88881,0.088646,0.44963,-92.617,0.3,-0.85423,-0.42461,385.43,0.34644,0.51229,-0.78584,222.39
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.88881,0.088646,0.44963,-119.95,0.3,-0.85423,-0.42461,407.89,0.34644,0.51229,-0.78584,232.56
> fitmap #5 inMap #1
Fit map RHdc in map rhlc using 258769 points
correlation = 0.7352, correlation about mean = 0.1434, overlap = 5.306e+05
steps = 228, shift = 30.3, angle = 17.5 degrees
Position of RHdc (#5) relative to rhlc (#1) coordinates:
Matrix rotation and translation
0.92400895 0.20809332 0.32078752 -128.41815383
0.36874013 -0.70694011 -0.60354487 407.59555942
0.10118390 0.67596809 -0.72995134 218.94888799
Axis 0.97812872 0.16787685 0.12280708
Axis point 0.00000000 172.43231180 196.09111463
Rotation angle (degrees) 139.15146292
Shift along axis -30.29515284
> hide #!5 models
> show #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.74755,0.45675,0.48223,-170.36,0.65388,-0.63358,-0.41354,278.58,0.11665,0.62446,-0.77229,234.78
> fitmap #5 inMap #1
Fit map RHdc in map rhlc using 258769 points
correlation = 0.7563, correlation about mean = 0.1303, overlap = 7.859e+05
steps = 768, shift = 1.59, angle = 4.61 degrees
Position of RHdc (#5) relative to rhlc (#1) coordinates:
Matrix rotation and translation
0.77383671 0.40931956 0.48335726 -168.65450172
0.62536997 -0.61477748 -0.48058407 296.31616029
0.10044470 0.67417071 -0.73171355 220.01909172
Axis 0.93455445 0.30989492 0.17485173
Axis point 0.00000000 134.52504155 182.18298735
Rotation angle (degrees) 141.84359142
Shift along axis -27.31922381
> hide #!1 models
> select add #5
3 models selected
> select add #5
3 models selected
> select add #5
3 models selected
> select add #5
3 models selected
> select add #5
3 models selected
> select clear
> view orient
> turn x 90
> turn y 5
> turn y -20
> view orient
> undo
> ui tool show "Side View"
> save /Users/chenxi/Desktop/RH-figure/map/rhdc.png width 2000 height 1241
> supersample 3 transparentBackground true
> turn x 90
> save /Users/chenxi/Desktop/RH-figure/map/rhdc-top.png width 2000 height 1241
> supersample 3 transparentBackground true
> hide #!5 models
> open /Users/chenxi/Desktop/RH_map-
> model/0808rhlip_all/rhlipc0808/rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb
Chain information for
rhlip_curve_apply_ncs_51_real_space_refined_053-coot-4.pdb #7
---
Chain | Description
A B C | No description available
> select add #7
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> color (#!7 & sel) byelement
> ui tool show "Color Actions"
> color sel bychain
> show #!1 models
> hide #!1 models
> hide #!7 models
> select subtract #7
Nothing selected
> show #!7 models
> show #!1 models
> color zone #1 near #7 distance 5.5
> color zone #1 near #7 distance 8.5
> color zone #1 near #7 distance 10.5
> hide #!7 models
> volume #1 level 0.2927
> save /Users/chenxi/Desktop/RH-figure/map/rhlc.png width 2000 height 1241
> supersample 3 transparentBackground true
> turn x 90
> volume #1 level 0.3152
> surface dust #1 size 11
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> volume #1 level 0.2815
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #5
3 models selected
> view matrix models
> #5,-0.63524,0.55892,0.533,141.2,0.75753,0.31651,0.57094,-159.78,0.15041,0.76644,-0.62445,164.87
> view matrix models
> #5,0.057497,-0.64519,-0.76186,500.89,-0.99704,-0.076113,-0.010789,486.98,-0.051026,0.76023,-0.64765,221.54
> select add #5
3 models selected
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> select add #5
3 models selected
> select add #5
3 models selected
> select add #5
3 models selected
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #5
3 models selected
> select clear
> hide #!2 models
> hide #!1 models
> show #!7 models
> select #7/A
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel burly wood
> color sel tan
> color sel burly wood
> color sel tan
> select #7/B
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel light steel blue
> color sel cornflower blue
> color sel sky blue
> color sel light steel blue
> select #7/C
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> color sel medium purple
> color sel light pink
> color sel pink
> ui tool show "Color Actions"
> color sel salmon
> color sel light pink
> color sel pink
> color sel light pink
> color sel thistle
> color sel light pink
> color sel light coral
> color sel dark salmon
> color sel salmon
> color sel light pink
> select add #7
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> select subtract #7
Nothing selected
> show #!1 models
> color zone #1 near #7 distance 10.5
> hide #!1 models
> show #!1 models
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> lighting flat
> hide #!1 models
> select #1/A
Nothing selected
> select #7/A
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color #7 #d7bb84ff
> undo
> ui tool show "Color Actions"
> color sel burly wood
> color sel rosy brown
> color sel tan
> color sel rosy brown
> color sel tan
> color sel burly wood
> select add #7
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> select subtract #7
Nothing selected
> show #!1 models
> select #7/A
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> ui tool show "Color Actions"
> color sel burly wood
> color sel tan
> color sel khaki
> color sel wheat
> color sel gold
> color sel yellow
> color sel dark salmon
> color sel burly wood
> color zone #1 near #7 distance 10.5
> select add #7
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> volume #1 level 0.2866
> volume #1 level 0.3067
> volume #1 level 0.2916
> view orient
> turn x 90
> turn y 5
> turn y -60
> save /Users/chenxi/Desktop/RH-figure/map/rhlc.png width 2000 height 1361
> supersample 3 transparentBackground true
> turn x 90
> show #!7 models
> select #7/A
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color (#!7 & sel) #ffe3ffff
> color (#!7 & sel) #ffe38bff
> select #7/B
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color (#!7 & sel) #a8e38bff
> color (#!7 & sel) #a8e08bff
> color (#!7 & sel) #a8e0eeff
> select #7/C
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color (#!7 & sel) #e8e0eeff
> color (#!7 & sel) #e88deeff
> color (#!7 & sel) #e88db2ff
> color zone #1 near #7 distance 10.5
> selct #7/A
Unknown command: selct #7/A
> select #7/A
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> select #7/A
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color (#!7 & sel) #ffb3ffff
> color (#!7 & sel) #ffcaffff
> color (#!7 & sel) #ffca80ff
> select #7/C
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> select #7/B
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color (#!7 & sel) #90ca80ff
> color (#!7 & sel) #907780ff
> color (#!7 & sel) #9077ffff
> color (#!7 & sel) #90b3ffff
> color zone #1 near #7 distance 10.5
> select #7/B
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> select #7/C
12535 atoms, 12840 bonds, 12 pseudobonds, 1513 residues, 2 models selected
> color (#!7 & sel) #f2b3ffff
> color (#!7 & sel) #f2a7ffff
> color (#!7 & sel) #f2a7bcff
> color zone #1 near #7 distance 10.5
> hide #!7 models
> show #!14 models
> hide #!14 models
> show #!5 models
> view orient
> turn x 90
> hide #!5 models
> select add #7
37605 atoms, 38520 bonds, 36 pseudobonds, 4539 residues, 2 models selected
> select subtract #7
Nothing selected
> turn x 90
> turn y 5
> show #!5 models
> select add #5
3 models selected
> view matrix models
> #5,0.12736,-0.65001,-0.74918,481.54,-0.99064,-0.12081,-0.063594,506.23,-0.049167,0.75026,-0.65931,225.7
> view matrix models
> #5,0.13774,-0.65428,-0.7436,478.51,-0.98766,-0.034207,-0.15285,508.97,0.074571,0.75548,-0.65092,191.96
> fitmap #5 inMap #1
Fit map RHdc in map rhlc using 258769 points
correlation = 0.7562, correlation about mean = 0.1304, overlap = 7.859e+05
steps = 184, shift = 7.51, angle = 6.76 degrees
Position of RHdc (#5) relative to rhlc (#1) coordinates:
Matrix rotation and translation
0.15473584 -0.73667900 -0.65830149 480.08196576
-0.98281310 -0.04688029 -0.17855145 517.43030904
0.10067374 0.67461563 -0.73127183 219.76449249
Axis 0.73037218 -0.64973720 -0.21070844
Axis point 0.00000000 425.23516581 288.75957033
Rotation angle (degrees) 144.26315999
Shift along axis -31.86144489
> hide #!1 models
> show #!6 models
> select add #5
3 models selected
> select add #5
3 models selected
> select add #6
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 5 models selected
> select add #5
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 5 models selected
> select add #5
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 5 models selected
> select clear
> select add #6
45516 atoms, 46656 bonds, 51 pseudobonds, 5571 residues, 2 models selected
> view matrix models
> #6,0.99281,-0.11336,-0.038456,33.731,-0.01455,-0.43315,0.9012,91.901,-0.11882,-0.89416,-0.43169,538.14
> view matrix models
> #6,0.9865,-0.040555,0.15865,-24.207,0.084202,-0.70531,-0.70388,485.94,0.14044,0.70774,-0.69237,202.99
> view matrix models
> #6,0.79354,0.33321,0.50919,-129.95,0.58293,-0.65634,-0.47896,295.5,0.17461,0.67689,-0.71507,205.57
> view matrix models
> #6,0.79104,0.32653,0.51734,-129.79,0.59129,-0.62504,-0.50961,293.89,0.15696,0.70901,-0.6875,197.34
> view matrix models
> #6,0.74114,0.37341,0.55792,-135.61,0.65116,-0.60209,-0.46203,262.88,0.16339,0.70573,-0.68938,196.76
> view matrix models
> #6,0.79632,0.32117,0.51257,-128.98,0.58435,-0.62738,-0.51472,297.33,0.15626,0.7094,-0.68727,197.39
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.79632,0.32117,0.51257,-158.76,0.58435,-0.62738,-0.51472,322.09,0.15626,0.7094,-0.68727,200.84
> view matrix models
> #6,0.79632,0.32117,0.51257,-155.5,0.58435,-0.62738,-0.51472,318.41,0.15626,0.7094,-0.68727,200.43
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.71383,0.39663,0.57717,-164.16,0.68017,-0.58892,-0.4365,267.95,0.16678,0.70417,-0.69017,199.43
> view matrix models
> #6,0.72542,0.42675,0.54005,-164.89,0.67806,-0.57797,-0.45408,270.25,0.11835,0.69558,-0.70863,217.93
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.72542,0.42675,0.54005,-169.72,0.67806,-0.57797,-0.45408,266.75,0.11835,0.69558,-0.70863,206.88
> fitmap #6 inMap #5
Fit molecule
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb (#6)
to map RHdc (#5) using 45516 atoms
average map value = 9.55, steps = 88
shifted from previous position = 3.43
rotated from previous position = 4.5 degrees
atoms outside contour = 21927, contour level = 8.1688
Position of
RH_detergent_apply_ncs_120-fit-j126-map_real_space_refined_129-coot-2.pdb (#6)
relative to RHdc (#5) coordinates:
Matrix rotation and translation
-0.48377066 0.73422967 0.47631163 116.57538856
-0.53391021 0.18364442 -0.82535730 488.15402543
-0.69347376 -0.65359128 0.30317095 466.05898207
Axis 0.09906882 0.67469255 -0.73142008
Axis point 282.90063316 412.93080079 0.00000000
Rotation angle (degrees) 119.89933278
Shift along axis 0.01796888
> show #!1 models
> select #6/A
14705 atoms, 15094 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> select #6/B
14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> color (#!6 & sel) #90a7bcff
> color (#!6 & sel) #90b3bcff
> color (#!6 & sel) #90b3ffff
> select #6/C
14702 atoms, 15091 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> color (#!6 & sel) #ffb3ffff
> color (#!6 & sel) #ffcaffff
> color (#!6 & sel) #ffca80ff
> hide #!1 models
> color zone #5 near #6 distance 30.5
> select #6/A
14705 atoms, 15094 bonds, 17 pseudobonds, 1848 residues, 2 models selected
> color (#!6 & sel) #f2ca80ff
> color (#!6 & sel) #f2a780ff
> color (#!6 & sel) #f2a7bcff
> color zone #5 near #6 distance 30.5
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> show #!1 models
> volume #2 level 0.3882
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #2 level 0.2323
> hide #!1 models
> volume #2 level 0.2355
> open /Users/chenxi/Desktop/0908/test70_Reference_002_Final.mrc
Opened test70_Reference_002_Final.mrc as #8, grid size 200,200,200, pixel 2.2,
shown at level 0.0175, step 1, values float32
> hide #!2 models
> volume #8 level 0.02102
> surface dust #2 size 11
> surface dust #8 size 22
> volume #2 level 0.2485
> hide #!2 models
> volume #8 level 0.01836
> volume #8 level 0.0178
> volume #8 level 0.01802
> hide #!8 models
> volume #2 level 0.2258
> volume #2 level 0.2355
> volume #2 level 0.2258
> volume #2 level 0.3135
> volume #2 level 0.268
> volume #2 level 0.2583
> volume #8 level 0.01847
> hide #!2 models
> volume #8 level 0.01836
> volume #8 level 0.01802
> show #!2 models
> volume #8 level 0.01869
> volume #2 level 0.229
> color #2 #f7faf8ff models
> color #2 #f4faf3ff models
> color #2 #fffaf3ff models
> color #2 #fffff3ff models
> color #2 white models
> show #!5 models
> color #5 #ffa5ffff models
> color #5 white models
> color zone #5 near #6 distance 30.5
> hide #!2 models
> volume #5 level 7.507
> color zone #5 near #6 distance28.5
Expected a keyword
> color zone #5 near #6 distance 28.5
> volume #5 level 8.06
> color zone #5 near #6 distance 25.5
> color zone #5 near #6 distance 20.5
> volume #5 level 7.508
> show #!6 models
> select clear
> select add #5
3 models selected
> color #5 darkgrey models
> color #5 white models
> color zone #5 near #6 distance 20.5
> select add #5
3 models selected
> select add #5
3 models selected
> select clear
> hide #!6 models
> color zone #5 near #6 distance 10.5
> color zone #5 near #6 distance 25.5
> show #!2 models
> open
> /Users/chenxi/Desktop/rhlip_flatten_apply_ncs_88_real_space_refined_091.pdb
Chain information for rhlip_flatten_apply_ncs_88_real_space_refined_091.pdb
#10
---
Chain | Description
A B C | No description available
> hide #!5 models
> hide #!10 models
> show #!10 models
> select add #10
34374 atoms, 35163 bonds, 39 pseudobonds, 4458 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.9913,0.13141,-0.0071661,-28.162,0.1097,-0.79499,0.59662,266.61,0.072707,-0.59222,-0.80249,561.27
> view matrix models
> #10,0.97934,0.14578,0.14015,-64.516,0.15289,-0.98738,-0.041301,457.33,0.13236,0.061876,-0.98927,435.31
> view matrix models
> #10,0.97694,0.21349,-0.00021558,-46.582,0.21328,-0.97603,-0.043412,442.11,-0.0094785,0.042365,-0.99906,472.9
> view matrix models
> #10,0.42445,0.90427,-0.046202,-83.596,0.88991,-0.42603,-0.16296,192.4,-0.16705,0.028054,-0.98555,507
> view matrix models
> #10,0.42077,0.90657,-0.032901,-86.561,0.89882,-0.42154,-0.12016,179.09,-0.1228,0.020987,-0.99221,500.8
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.42077,0.90657,-0.032901,-58.75,0.89882,-0.42154,-0.12016,143.54,-0.1228,0.020987,-0.99221,508.95
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.016115,0.99891,0.043764,-5.5293,0.98715,0.022855,-0.15817,26.29,-0.159,0.040652,-0.98644,510.6
> view matrix models
> #10,-0.039881,0.99916,-0.0089349,12.205,0.99909,0.039739,-0.01548,-14.701,-0.015112,-0.0095441,-0.99984,495
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.039881,0.99916,-0.0089349,11.858,0.99909,0.039739,-0.01548,-6.8199,-0.015112,-0.0095441,-0.99984,495.18
> fitmap #10 inMap #2
Fit molecule rhlip_flatten_apply_ncs_88_real_space_refined_091.pdb (#10) to
map J1594_005_volume_map_sharp.mrc (#2) using 34374 atoms
average map value = 0.2808, steps = 68
shifted from previous position = 2.4
rotated from previous position = 2.74 degrees
atoms outside contour = 15208, contour level = 0.22902
Position of rhlip_flatten_apply_ncs_88_real_space_refined_091.pdb (#10)
relative to J1594_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.50351885 -0.86398423 0.00004941 519.88323227
0.86398423 -0.50351884 -0.00001114 140.43495080
0.00003450 0.00003708 0.99999998 -1.50311009
Axis 0.00002791 0.00000863 1.00000000
Axis point 219.59176253 219.59071739 0.00000000
Rotation angle (degrees) 120.23308016
Shift along axis -1.48739086
> show #!1 models
> select subtract #10
Nothing selected
> select #10/A
11458 atoms, 11721 bonds, 13 pseudobonds, 1486 residues, 2 models selected
> color (#!10 & sel) #f2ffffff
> color (#!10 & sel) #f2a7ffff
> color (#!10 & sel) #f2a7bcff
> select #10/B
11458 atoms, 11721 bonds, 13 pseudobonds, 1486 residues, 2 models selected
> color (#!10 & sel) #90a7bcff
> color (#!10 & sel) #90b3bcff
> color (#!10 & sel) #90b3ffff
> select #10/C
11458 atoms, 11721 bonds, 13 pseudobonds, 1486 residues, 2 models selected
> color (#!10 & sel) #ffb3ffff
> color (#!10 & sel) #ffcaffff
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLXY3CH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 41天14小时54分钟
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
YOGA27_APH8:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 1280 x 720 @ 60.00Hz
Main Display: Yes
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 , 7 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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