![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#18023 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-15.3.2-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 0x00000001f257c840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 65)
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 3379,
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"build" : "24D81",
"releaseType" : "User"
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"captureTime" : "2025-06-18 09:35:34.8950 -0400",
"codeSigningMonitor" : 1,
"incident" : "43B799FC-6148-4B3E-91E9-C7EA32BFFF10",
"pid" : 31637,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-18 08:04:32.2607 -0400",
"procStartAbsTime" : 2690059162070,
"procExitAbsTime" : 2812188656149,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "8D5BA149-0422-1D1A-10AD-23D6A9E1891D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "442AE5D0-96C3-416B-BDF9-68A3A4E1F42D",
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"exception" : {"codes":"0x0000000000000001, 0x00008d74c511eec8","rawCodes":[1,155532662009544],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00008d74c511eec8 -> 0x00000d74c511eec8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31637},
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Address size fault"},"pc":{"value":6589048556},"far":{"value":0}}},{"id":7613823,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":191}],"threadState":{"x":[{"value":14113222656},{"value":144831},{"value":14112686080},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":14113222656},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6589280488},"far":{"value":0}}},{"id":7623521,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":191}],"threadState":{"x":[{"value":13864972288},{"value":162419},{"value":13864435712},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13864972288},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6589280488},"far":{"value":0}}},{"id":7623522,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":191}],"threadState":{"x":[{"value":13933146112},{"value":164987},{"value":13932609536},{"value":0},{"value":409602},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13933146112},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6589280488},"far":{"value":0}}},{"id":7625557,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":191}],"threadState":{"x":[{"value":13939044352},{"value":112695},{"value":13938507776},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13939044352},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6589280488},"far":{"value":0}}},{"id":7625558,"threadState":{"x":[{"value":105560062911296},{"value":0},{"value":65544},{"value":1},{"value":8360819568,"symbolLocation":40,"symbol":"_OS_dispatch_source_vtable"},{"value":16},{"value":0},{"value":0},{"value":3238002689},{"value":4294967294},{"value":3238002690},{"value":2},{"value":3238002689},{"value":105560062911304},{"value":3238002690},{"value":2181095450},{"value":6586146136,"symbolLocation":0,"symbol":"_Block_release"},{"value":8501581888},{"value":0},{"value":0},{"value":105560062911296},{"value":65544},{"value":105597838109568},{"value":105553293071104},{"value":105553147058104},{"value":105553142088960},{"value":65544},{"value":0},{"value":8360821824,"symbolLocation":0,"symbol":"_dispatch_mgr_q"}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6586146964},"cpsr":{"value":1610616832},"fp":{"value":13940598624},"sp":{"value":13940598576},"esr":{"value":2449473543,"description":"(Data Abort) byte read Translation fault"},"pc":{"value":6586147172},"far":{"value":0}},"queue":"com.apple.CFMachPort","frames":[{"imageOffset":8548,"symbol":"_call_custom_dispose_helper","symbolLocation":64,"imageIndex":202},{"imageOffset":8340,"symbol":"_call_dispose_helpers_excp","symbolLocation":48,"imageIndex":202},{"imageOffset":7768,"symbol":"_Block_release","symbolLocation":256,"imageIndex":202},{"imageOffset":113264,"symbol":"_dispatch_source_handler_dispose","symbolLocation":36,"imageIndex":196},{"imageOffset":111548,"symbol":"_dispatch_source_cancel_callout","symbolLocation":88,"imageIndex":196},{"imageOffset":109204,"symbol":"_dispatch_source_invoke","symbolLocation":908,"imageIndex":196},{"imageOffset":47672,"symbol":"_dispatch_lane_serial_drain","symbolLocation":352,"imageIndex":196},{"imageOffset":50992,"symbol":"_dispatch_lane_invoke","symbolLocation":380,"imageIndex":196},{"imageOffset":96672,"symbol":"_dispatch_root_queue_drain_deferred_wlh","symbolLocation":288,"imageIndex":196},{"imageOffset":94700,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":540,"imageIndex":196},{"imageOffset":13272,"symbol":"_pthread_wqthread","symbolLocation":288,"imageIndex":191},{"imageOffset":8432,"symbol":"start_wqthread","symbolLocation":8,"imageIndex":191}]}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6584795136,
"size" : 4865835008,
"uuid" : "5700d77a-6190-36e0-884d-fee6d586d62f"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=111.1G written=56.1M(0%) resident=56.1M(0%) swapped_out=0K(0%) unallocated=111.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1088K 45 \nColorSync 656K 33 \nCoreAnimation 3120K 183 \nCoreGraphics 48K 3 \nCoreUI image data 3568K 49 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 109.9G 457 \nMALLOC guard page 288K 18 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 40 \nStack 193.4M 40 \nVM_ALLOCATE 449.9M 361 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 5289K 673 \n__AUTH_CONST 70.9M 921 \n__CTF 824 1 \n__DATA 34.4M 1102 \n__DATA_CONST 34.9M 1118 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 644.5M 191 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1138 \n__TPRO_CONST 272K 2 \ndyld private memory 304K 3 \nmapped file 541.4M 79 \nowned unmapped memory 206.7M 1 \npage table in kernel 56.1M 1 \nshared memory 3232K 29 \n=========== ======= ======= \nTOTAL 113.7G 6851 \nTOTAL, minus reserved VM space 113.5G 6851 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "c60400b0e9e1e862b3b8b26f11939280986ec8fb",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "654439cdafbf5b61207873a9",
"factorPackIds" : {
},
"deploymentId" : 240000004
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{
"rolloutId" : "60356660bbe37970735c5624",
"factorPackIds" : {
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"experiments" : [
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/fitting.cxs
Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32
Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32
Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32
Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 0.15, step 1, values float32
Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.108, step 1, values float32
Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened Medi8897_Site0_red.mrc as #10, grid size 208,208,208, pixel 2, shown at
level 0.0929, step 1, values float32
Opened RSV monomer.mrc as #11, grid size 208,208,208, pixel 2, shown at level
0.1, step 1, values float32
Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #16, grid size
208,208,208, pixel 2, shown at level 1.16, step 1, values float32
Opened cryosparc_P141_J36_001_volume_map.mrc as #15, grid size 208,208,208,
pixel 2, shown at level 1.04, step 1, values float32
Log from Tue Jun 17 10:45:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs
Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32
Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32
Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32
Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 0.15, step 1, values float32
Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32
Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened Medi8897_Site0_red.mrc as #10, grid size 208,208,208, pixel 2, shown at
level 0.03, step 1, values float32
Opened RSV monomer.mrc as #11, grid size 208,208,208, pixel 2, shown at level
0.026, step 1, values float32
Log from Mon Jun 16 08:40:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs
Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32
Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32
Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32
Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 0.15, step 1, values float32
Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32
Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32
Log from Thu May 8 15:20:48 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/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/101F_SiteIV_purple.mrc
Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 1.84e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/A14_V_Orange.mrc
Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
1.84e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/ADI-14442_SiteV-II_orange-yellow.mrc
Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 1.83e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/D25_Site0_red.mrc
Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
1.84e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/Motavizumab_SiteII_yellow.mrc
Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 1.84e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/MPE8_SiteIII_green.mrc
Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 1.84e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/MPE8_SiteIII_purple.mrc
Opened MPE8_SiteIII_purple.mrc as #7, grid size 208,208,208, pixel 2, shown at
level 1.84e-05, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.000161, step 1, values float32
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/RSB1_SiteV_orange.mrc
Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 1.76e-05, step 1, values float32
> lighting soft
> select clear
> volume all level 0.15
> select #8
2 models selected
> color #8.1 gray
> set bgColor white
> color #8.1 light gray
> select #1
2 models selected
> color #1.1 purple
> select #4
2 models selected
> color #4.1 red
> select #3
2 models selected
> ui tool show "Color Actions"
> color sel orange
No visible atoms or bonds selected
[Repeated 13 time(s)]
> select #5
2 models selected
> color #5.1 yellow
> select #2
2 models selected
> color #2.1 orange
> select #9
2 models selected
> color #9.1 orange
> select #3
2 models selected
> ui tool show "Color Actions"
> color sel gold
> color sel sandy brown
> color sel dark orange
> color sel gold
> select #5
2 models selected
> ui tool show "Color Actions"
> color sel gold
> color sel yellow
[Repeated 1 time(s)]
> select clear
> select #6
2 models selected
> color #6.1 forest green
> select clear
> select #6
2 models selected
> color #6.1 forest green
> ui tool show "Color Actions"
> color sel forest green
> color sel green
> color sel dodger blue
> color sel turquoise
> volume #7 color #5eaf88
> volume #7 color #00f900
> color sel forest green
[Repeated 1 time(s)]
> color #6.1 forest green
> close #7
> ui mousemode right zoom
> select clear
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/front.png" width 936 height 671
> supersample 3 transparentBackground true
> hide #!4 models
> show #!4 models
> graphics silhouettes true
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/TopView.png" width 936 height 671
> supersample 3 transparentBackground true
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/front.png" width 936 height 671
> supersample 3 transparentBackground true
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/SideView.png" width 936 height 671
> supersample 3 transparentBackground true
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!5 models
> hide #!3 models
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/front.png" width 936 height 671
> supersample 3 transparentBackground true
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/SideView.png" width 936 height 671
> supersample 3 transparentBackground true
> hide #!4 models
> show #!4 models
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/TopView.png" width 936 height 671
> supersample 3 transparentBackground true
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true
——— End of log from Thu May 8 15:20:48 2025 ———
opened ChimeraX session
> show #!2 models
> open /Users/szhang3/Downloads/5udc.pdb
5udc.pdb title:
Crystal structure of RSV F A2 bound to MEDI8897 [more info...]
Chain information for 5udc.pdb #7
---
Chain | Description | UniProt
A D F | protein F | FUS_HRSVA 1-513
B E H | MEDI8897 fab heavy chain |
C G L | MEDI8897 fab light chain |
Non-standard residues in 5udc.pdb #7
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
CL — chloride ion
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide atoms
> hide cartoons
> show cartoons
> select add #7
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected
> select subtract #7
Nothing selected
> select add #7
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.88918,0.059463,0.45368,10.939,0.43217,-0.43489,-0.79,43.97,0.15033,0.89852,-0.41239,-85.347
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.88918,0.059463,0.45368,122.68,0.43217,-0.43489,-0.79,296.84,0.15033,0.89852,-0.41239,5.384
> view matrix models
> #7,0.88918,0.059463,0.45368,171.33,0.43217,-0.43489,-0.79,179.17,0.15033,0.89852,-0.41239,201.23
> view matrix models
> #7,0.88918,0.059463,0.45368,240.03,0.43217,-0.43489,-0.79,163.15,0.15033,0.89852,-0.41239,168.21
> ui tool show "Fit in Map"
> fitmap #7 inMap #8
Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
using 20324 atoms
average map value = 0.1316, steps = 112
shifted from previous position = 8.08
rotated from previous position = 18.1 degrees
atoms outside contour = 10579, contour level = 0.15
Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
(#8) coordinates:
Matrix rotation and translation
0.82604493 0.02497455 0.56305066 249.73640605
0.55945921 -0.15727372 -0.81379996 158.97442632
0.06822879 0.98723920 -0.14388740 179.75571678
Axis 0.92705817 0.25470221 0.27511804
Axis point 0.00000000 6.52392129 85.45899564
Rotation angle (degrees) 103.74246189
Shift along axis 321.46535400
> select clear
> hide #!9 models
> hide #!8 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!6 models
> hide #!5 models
Drag select of 470 residues
> select up
4639 atoms, 4727 bonds, 603 residues, 1 model selected
> select up
10429 atoms, 10603 bonds, 1345 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!8 models
> show #!4 models
Drag select of 72 residues
> select up
773 atoms, 780 bonds, 106 residues, 1 model selected
> select up
1618 atoms, 1659 bonds, 217 residues, 1 model selected
> select add /L:126
1627 atoms, 1667 bonds, 218 residues, 1 model selected
Drag select of 110 residues
> select up
3121 atoms, 3182 bonds, 416 residues, 1 model selected
> select up
6517 atoms, 6670 bonds, 861 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!4 models
Drag select of 287 residues, 1 pseudobonds
> select up
2458 atoms, 2510 bonds, 1 pseudobond, 326 residues, 2 models selected
> select up
3249 atoms, 3326 bonds, 1 pseudobond, 429 residues, 2 models selected
> select up
3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected
> select up
3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected
> vop gaussian #7 sd 3
> molmap #7 20 onGrid #8
Opened 5udc.pdb map 20 as #10, grid size 208,208,208, pixel 2, shown at level
0.0257, step 1, values float32
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select #10
2 models selected
> select clear
Drag select of 10 5udc.pdb map 20
> select clear
> select #10
2 models selected
> select clear
> hide #!10 models
> select add #7
3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected
> show sel atoms
Drag select of 76 atoms, 84 bonds
> select up
82 atoms, 87 bonds, 8 residues, 1 model selected
> select up
88 atoms, 94 bonds, 8 residues, 1 model selected
> select up
127 atoms, 137 bonds, 11 residues, 1 model selected
> select up
3378 atoms, 3463 bonds, 442 residues, 1 model selected
> select down
127 atoms, 137 bonds, 11 residues, 1 model selected
> hide #!8 models
> select clear
Drag select of 1 atoms
Drag select of 6 atoms, 6 bonds
Drag select of 1 atoms
> select up
12 atoms, 7 bonds, 5 residues, 1 model selected
> select up
38 atoms, 37 bonds, 5 residues, 1 model selected
> select up
129 atoms, 137 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!8 models
> hide atoms
> show cartoons
> molmap #7 20 onGrid #8
Opened 5udc.pdb map 20 as #10, grid size 208,208,208, pixel 2, shown at level
0.03, step 1, values float32
> show #!4 models
> color #10 #ff2600ff models
> hide #!8 models
> show #!8 models
> hide #!7 models
> close #7
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/Medi8897_Site0_red.mrc" models #10
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> ui mousemode right zoom
> rock axis y
> movie record
> movie encode /Users/szhang3/Desktop/movie2.mp4
Movie saved to /Users/szhang3/Desktop/movie2.mp4
> stop
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/RSV_MEDI_Mota.png" width 936 height 665
> supersample 3 transparentBackground true
> open /Users/szhang3/Downloads/5udc.pdb
5udc.pdb title:
Crystal structure of RSV F A2 bound to MEDI8897 [more info...]
Chain information for 5udc.pdb #7
---
Chain | Description | UniProt
A D F | protein F | FUS_HRSVA 1-513
B E H | MEDI8897 fab heavy chain |
C G L | MEDI8897 fab light chain |
Non-standard residues in 5udc.pdb #7
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
CL — chloride ion
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide atoms
> show cartoons
> select add #7
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.45186,0.83609,0.31109,-39.974,0.59179,-0.019992,-0.80585,30.737,-0.66754,0.54823,-0.50382,-98.435
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.45186,0.83609,0.31109,10.706,0.59179,-0.019992,-0.80585,229.92,-0.66754,0.54823,-0.50382,-81.952
> view matrix models
> #7,0.45186,0.83609,0.31109,179.34,0.59179,-0.019992,-0.80585,158.03,-0.66754,0.54823,-0.50382,186.41
> view matrix models
> #7,0.45186,0.83609,0.31109,204.92,0.59179,-0.019992,-0.80585,146.3,-0.66754,0.54823,-0.50382,186.25
> view matrix models
> #7,0.45186,0.83609,0.31109,199.52,0.59179,-0.019992,-0.80585,144.61,-0.66754,0.54823,-0.50382,185.8
> view matrix models
> #7,0.45186,0.83609,0.31109,191.86,0.59179,-0.019992,-0.80585,143.65,-0.66754,0.54823,-0.50382,176.83
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.45386,0.75421,0.47453,201.39,0.72149,0.0014847,-0.69242,150.81,-0.52294,0.65663,-0.54348,175.14
> fitmap #7 inMap #8
Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
using 20324 atoms
average map value = 0.1316, steps = 236
shifted from previous position = 23.1
rotated from previous position = 48.8 degrees
atoms outside contour = 10580, contour level = 0.15
Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
(#8) coordinates:
Matrix rotation and translation
0.82584349 0.02466872 0.56335955 249.77298201
0.55968844 -0.15772236 -0.81355547 159.01791335
0.06878502 0.98717532 -0.14406078 179.73879837
Axis 0.92699562 0.25460131 0.27542203
Axis point 0.00000000 6.62206876 85.41492505
Rotation angle (degrees) 103.76674887
Shift along axis 321.52865406
> select clear
> ui mousemode right zoom
> hide #!8 models
> select /A:225
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
218 atoms, 219 bonds, 26 residues, 1 model selected
> select up
3474 atoms, 3532 bonds, 448 residues, 1 model selected
> select ~sel & ##selected
16850 atoms, 17205 bonds, 5 pseudobonds, 2200 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> vop gaussian #7 sd 3
> molmap #7 20 onGrid #8
Opened 5udc.pdb map 20 as #11, grid size 208,208,208, pixel 2, shown at level
0.026, step 1, values float32
> save "/Users/szhang3/OneDrive - Moderna/RSV/EMPEM/EMPEMcomposition/RSV
> monomer.mrc" models #11
> color #11 #ebebebff models
> color #11 silver models
> color #11 #d6d6d6ff models
> color #11 silver models
> color #11 darkgrey models
> color #11 #d6d6d6ff models
> color #11 silver models
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true
——— End of log from Mon Jun 16 08:40:41 2025 ———
opened ChimeraX session
> open /Users/szhang3/Downloads/cryosparc_P141_J26_002_volume_map_sharp.mrc
Opened cryosparc_P141_J26_002_volume_map_sharp.mrc as #12, grid size
208,208,208, pixel 2, shown at level 0.127, step 1, values float32
> volume #12 level 0.5003
> color #12 #8671ffff models
> color #12 #7974d0ff models
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #12
2 models selected
> view matrix models #12,1,0,0,-20.113,0,1,0,6.1289,0,0,1,-81.251
> volume #12 level 0.7243
> view matrix models #12,1,0,0,-72.319,0,1,0,-7.8902,0,0,1,-117.41
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.85671,0.51448,0.036776,-161.49,-0.23388,0.32393,0.91672,11.617,0.45972,-0.79397,0.39784,75.407
> view matrix models
> #12,-0.23839,-0.95776,0.16081,360.59,0.22332,0.10708,0.96884,-45.696,-0.94514,0.26687,0.18837,175.29
> view matrix models
> #12,-0.20038,-0.513,-0.83467,446.85,-0.31028,0.84133,-0.4426,175.42,0.92929,0.1703,-0.32776,-91.96
> view matrix models
> #12,0.55647,0.37463,-0.74162,79.981,-0.76613,-0.11406,-0.63248,513.39,-0.32154,0.92013,0.22354,-102.08
> view matrix models
> #12,0.45813,0.27593,-0.84497,141.52,0.063477,0.93802,0.34073,-72.806,0.88662,-0.20974,0.41222,-142.37
> view matrix models
> #12,0.28731,0.74605,-0.60072,27.923,-0.46436,0.65702,0.59388,48.721,0.83775,0.10832,0.5352,-224.9
> view matrix models
> #12,0.44323,0.7968,-0.41067,-51.703,-0.25285,0.55065,0.79552,-10.483,0.86001,-0.24876,0.44554,-134.78
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.44323,0.7968,-0.41067,-150.03,-0.25285,0.55065,0.79552,-15.976,0.86001,-0.24876,0.44554,-117.73
> view matrix models
> #12,0.44323,0.7968,-0.41067,-158.11,-0.25285,0.55065,0.79552,-12.325,0.86001,-0.24876,0.44554,-115.58
> view matrix models
> #12,0.44323,0.7968,-0.41067,-144.76,-0.25285,0.55065,0.79552,-9.0075,0.86001,-0.24876,0.44554,-117.02
> view matrix models
> #12,0.44323,0.7968,-0.41067,-140.49,-0.25285,0.55065,0.79552,-11.642,0.86001,-0.24876,0.44554,-118.23
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.24134,0.81643,-0.5246,-81.23,-0.76619,0.49206,0.41331,180.3,0.59557,0.3022,0.74429,-240.48
> volume flip #12
Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip as #13, grid size
208,208,208, pixel 2, shown at step 1, values float32
> view matrix models
> #12,0.24134,0.81643,-0.5246,-81.23,-0.76619,0.49206,0.41331,180.3,0.59557,0.3022,0.74429,-240.48
> select subtract #12
Nothing selected
> select add #13
2 models selected
> view matrix models
> #13,0.88137,0.42106,0.21422,-291.9,0.24243,-0.013906,-0.97007,389.62,-0.40548,0.90692,-0.11433,25.925
> view matrix models
> #13,0.9139,0.36932,0.16849,-277.21,0.18036,0.0024284,-0.9836,401.9,-0.36368,0.9293,-0.064391,1.324
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.9139,0.36932,0.16849,-103.5,0.18036,0.0024284,-0.9836,361.38,-0.36368,0.9293,-0.064391,155.05
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.4012,0.89607,0.18997,-116.79,0.23152,0.10146,-0.96752,325.73,-0.88625,0.43216,-0.16676,393.69
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.4012,0.89607,0.18997,-80.842,0.23152,0.10146,-0.96752,334.88,-0.88625,0.43216,-0.16676,370.81
> view matrix models
> #13,0.4012,0.89607,0.18997,-77.197,0.23152,0.10146,-0.96752,339.63,-0.88625,0.43216,-0.16676,370.62
> view matrix models
> #13,0.4012,0.89607,0.18997,-72.508,0.23152,0.10146,-0.96752,338.25,-0.88625,0.43216,-0.16676,369.84
> view matrix models
> #13,0.4012,0.89607,0.18997,-75.103,0.23152,0.10146,-0.96752,341.42,-0.88625,0.43216,-0.16676,364.46
> view matrix models
> #13,0.4012,0.89607,0.18997,-73.383,0.23152,0.10146,-0.96752,335.6,-0.88625,0.43216,-0.16676,361.95
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.37548,0.87546,0.30426,-89.02,0.062866,0.30347,-0.95077,322.83,-0.92469,0.37613,0.058911,331.85
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.37548,0.87546,0.30426,-86.58,0.062866,0.30347,-0.95077,332.72,-0.92469,0.37613,0.058911,323.22
> view matrix models
> #13,0.37548,0.87546,0.30426,-90.558,0.062866,0.30347,-0.95077,327.08,-0.92469,0.37613,0.058911,329.22
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!5 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> select subtract #13
Nothing selected
> hide #!13 models
> close #7
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/5udc.pdb
5udc.pdb title:
Crystal structure of RSV F A2 bound to MEDI8897 [more info...]
Chain information for 5udc.pdb #7
---
Chain | Description | UniProt
A D F | protein F | FUS_HRSVA 1-513
B E H | MEDI8897 fab heavy chain |
C G L | MEDI8897 fab light chain |
Non-standard residues in 5udc.pdb #7
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
CL — chloride ion
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> show #!12 models
> select add #7
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected
> view matrix models #7,1,0,0,-0.48937,0,1,0,0.39238,0,0,1,-0.16138
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.33025,-0.94288,-0.043795,17.219,0.75655,0.29216,-0.58504,32.068,0.56442,0.16008,0.80982,3.4109
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.33025,-0.94288,-0.043795,70.064,0.75655,0.29216,-0.58504,196.92,0.56442,0.16008,0.80982,116.9
> hide #!12 models
> show #!12 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.58369,0.038922,-0.81105,-28.025,0.59983,0.6939,-0.39838,181.97,0.54728,-0.71902,-0.42837,107.88
> view matrix models
> #7,-0.81759,0.15848,-0.55357,-30.782,0.38013,0.87067,-0.31216,170.9,0.4325,-0.46564,-0.77209,80.908
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.81759,0.15848,-0.55357,-41.559,0.38013,0.87067,-0.31216,158.57,0.4325,-0.46564,-0.77209,64.634
> view matrix models
> #7,-0.81759,0.15848,-0.55357,-39.222,0.38013,0.87067,-0.31216,174.81,0.4325,-0.46564,-0.77209,55.488
> volume #12 level 1.602
> volume #13 level 1.565
> view matrix models
> #7,-0.81759,0.15848,-0.55357,-53.214,0.38013,0.87067,-0.31216,183.83,0.4325,-0.46564,-0.77209,47.115
> view matrix models
> #7,-0.81759,0.15848,-0.55357,-46.239,0.38013,0.87067,-0.31216,184.8,0.4325,-0.46564,-0.77209,49.871
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.5328,-0.64649,-0.54605,-3.0846,0.1861,0.53996,-0.82086,174.05,0.82552,-0.53898,-0.16738,87.422
> view matrix models
> #7,-0.49607,-0.72907,-0.47156,4.2976,0.14473,0.46607,-0.87283,173.98,0.85614,-0.50123,-0.12568,88.305
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.49607,-0.72907,-0.47156,2.3478,0.14473,0.46607,-0.87283,152.19,0.85614,-0.50123,-0.12568,103.79
> view matrix models
> #7,-0.49607,-0.72907,-0.47156,6.4068,0.14473,0.46607,-0.87283,153.02,0.85614,-0.50123,-0.12568,103.74
> select add #13
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 4 models selected
> select subtract #13
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected
> select add #13
20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 4 models selected
> view matrix models
> #13,0.37548,0.87546,0.30426,-154.4,0.062866,0.30347,-0.95077,275.45,-0.92469,0.37613,0.058911,339.16,#7,-0.49607,-0.72907,-0.47156,-57.439,0.14473,0.46607,-0.87283,101.39,0.85614,-0.50123,-0.12568,113.68
> undo
> select subtract #7
2 models selected
> view matrix models
> #13,0.37548,0.87546,0.30426,-191.16,0.062866,0.30347,-0.95077,228.01,-0.92469,0.37613,0.058911,330.85
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.33423,0.89314,0.301,-185.77,0.067552,0.29584,-0.95285,229.16,-0.94007,0.3388,0.038545,346.64
> view matrix models
> #13,0.12428,0.5826,0.8032,-186.54,0.51428,0.65444,-0.55427,-29.345,-0.84857,0.48196,-0.21828,353.71
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.12428,0.5826,0.8032,-344.99,0.51428,0.65444,-0.55427,21.857,-0.84857,0.48196,-0.21828,235.47
> view matrix models
> #13,0.12428,0.5826,0.8032,-273.8,0.51428,0.65444,-0.55427,86.696,-0.84857,0.48196,-0.21828,229.83
> view matrix models
> #13,0.12428,0.5826,0.8032,-295.86,0.51428,0.65444,-0.55427,103.05,-0.84857,0.48196,-0.21828,196.19
> color #13 #73fcd6ff models
> color #13 #db8976ff models
> view matrix models
> #13,0.12428,0.5826,0.8032,-304.83,0.51428,0.65444,-0.55427,105.98,-0.84857,0.48196,-0.21828,188.31
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.72756,0.46178,0.50736,-337.33,0.48255,0.1812,-0.85692,282.49,-0.48764,0.86829,-0.090993,1.7161
> view matrix models
> #13,0.73719,0.45306,0.50129,-336.07,0.47587,0.17858,-0.8612,285.39,-0.47969,0.87341,-0.083949,-2.6001
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.73719,0.45306,0.50129,-339.81,0.47587,0.17858,-0.8612,276.72,-0.47969,0.87341,-0.083949,7.9467
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.59842,0.5518,0.58087,-350.3,0.54223,0.2548,-0.80066,233.04,-0.58981,0.7941,-0.14673,61.822
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.59842,0.5518,0.58087,-347.08,0.54223,0.2548,-0.80066,226.03,-0.58981,0.7941,-0.14673,60.999
> hide atoms
> show cartoons
> volume #12 level 1.975
> volume #13 level 1.733
> volume #13 level 1.817
> hide #!13 models
> hide #!12 models
> select subtract #13
Nothing selected
> show #!13 models
> show #!12 models
Drag select of 162 residues
> select up
1754 atoms, 1781 bonds, 237 residues, 1 model selected
> select up
3249 atoms, 3326 bonds, 429 residues, 1 model selected
Drag select of 316 residues, 1 pseudobonds
> select up
6093 atoms, 6231 bonds, 1 pseudobond, 803 residues, 2 models selected
> select up
6529 atoms, 6683 bonds, 1 pseudobond, 862 residues, 2 models selected
> hide #!12 models
> hide #!13 models
> view matrix models
> #7,-0.49607,-0.72907,-0.47156,6.7596,0.14473,0.46607,-0.87283,155.05,0.85614,-0.50123,-0.12568,105.98
> select add /A:209
6538 atoms, 6691 bonds, 1 pseudobond, 863 residues, 2 models selected
> select add /D:206
6546 atoms, 6698 bonds, 1 pseudobond, 864 residues, 2 models selected
> select up
6659 atoms, 6813 bonds, 1 pseudobond, 878 residues, 2 models selected
> select up
13476 atoms, 13746 bonds, 1 pseudobond, 1758 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> show #!12 models
> hide #!12 models
> show #!13 models
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/4zyp_Mota_AM14.pdb
4zyp_Mota_AM14.pdb title:
Crystal structure of motavizumab and quaternary-specific RSV- neutralizing
human antibody AM14 In complex with prefusion RSV F glycoprotein [more
info...]
Chain information for 4zyp_Mota_AM14.pdb #14
---
Chain | Description | UniProt
A B C | protein F | FUS_HRSVA 26-513, D9IEJ2_BPT4 518-544
D F H | AM14 antibody fab heavy chain |
E G I | AM14 antibody light chain |
J K N | motavizumab antibody fab heavy chain |
L M O | motavizumab antibody light chain |
> hide atoms
> show cartoons
Drag select of 102 residues, 1 pseudobonds
> select up
2138 atoms, 2158 bonds, 1 pseudobond, 266 residues, 2 models selected
> select up
10446 atoms, 10621 bonds, 1 pseudobond, 1347 residues, 2 models selected
> select add #7/F:313
10452 atoms, 10626 bonds, 1 pseudobond, 1348 residues, 3 models selected
> select up
10537 atoms, 10715 bonds, 1 pseudobond, 1358 residues, 3 models selected
> select up
13928 atoms, 14161 bonds, 1 pseudobond, 1796 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!14 & sel to #7 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5udc.pdb, chain F (#7) with 4zyp_Mota_AM14.pdb, chain C (#14),
sequence alignment score = 2359
RMSD between 436 pruned atom pairs is 0.589 angstroms; (across all 448 pairs:
1.048)
> select clear
> hide #!13 models
> hide #!7 models
> show #!7 models
> show #!2 models
> show #!11 models
> hide #!11 models
> show #!8 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> select add #7
6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 2 models selected
> select add #14
36838 atoms, 37648 bonds, 11 pseudobonds, 4796 residues, 4 models selected
> select add #13
36838 atoms, 37648 bonds, 11 pseudobonds, 4796 residues, 6 models selected
> select add #12
36838 atoms, 37648 bonds, 11 pseudobonds, 4796 residues, 8 models selected
> show #!11 models
> hide #!11 models
> view matrix models
> #12,0.24134,0.81643,-0.5246,91.851,-0.76619,0.49206,0.41331,243.17,0.59557,0.3022,0.74429,-211.07,#13,0.59842,0.5518,0.58087,-174,0.54223,0.2548,-0.80066,288.89,-0.58981,0.7941,-0.14673,90.411,#7,-0.49607,-0.72907,-0.47156,179.84,0.14473,0.46607,-0.87283,217.92,0.85614,-0.50123,-0.12568,135.39,#14,-0.26307,-0.89838,0.35173,183.77,-0.96224,0.21793,-0.16307,336.3,0.069848,-0.38135,-0.92179,126.27
> view matrix models
> #12,0.24134,0.81643,-0.5246,45.145,-0.76619,0.49206,0.41331,175.54,0.59557,0.3022,0.74429,-132.99,#13,0.59842,0.5518,0.58087,-220.71,0.54223,0.2548,-0.80066,221.27,-0.58981,0.7941,-0.14673,168.49,#7,-0.49607,-0.72907,-0.47156,133.13,0.14473,0.46607,-0.87283,150.29,0.85614,-0.50123,-0.12568,213.47,#14,-0.26307,-0.89838,0.35173,137.06,-0.96224,0.21793,-0.16307,268.67,0.069848,-0.38135,-0.92179,204.34
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.22885,0.90859,-0.34943,-5.3538,-0.47921,0.4176,0.77199,64.106,0.84734,-0.0092161,0.53097,-77.574,#13,0.56675,0.69313,0.44538,-214.7,0.13098,0.4579,-0.8793,277.89,-0.81341,0.55668,0.16873,194.7,#7,-0.33879,-0.73097,-0.59237,129.93,0.57383,0.33842,-0.74579,169.69,0.74562,-0.59258,0.3048,237.02,#14,-0.36988,-0.91046,0.18505,147.48,-0.78177,0.19737,-0.59151,270.76,0.50203,-0.36346,-0.78477,177.09
> show #!10 models
> view matrix models
> #12,0.50691,0.81558,-0.27904,-53.924,-0.41972,0.51628,0.74651,38.813,0.75291,-0.2613,0.60403,-25.435,#13,0.30281,0.76015,0.57488,-204.36,0.16439,0.5525,-0.81714,237.42,-0.93877,0.34194,0.042342,293.29,#7,-0.18677,-0.89987,-0.39415,148.93,0.55865,0.23274,-0.79608,170.16,0.8081,-0.36888,0.45924,239.17,#14,-0.12353,-0.99184,0.031387,137.36,-0.79976,0.080783,-0.59487,270.34,0.58748,-0.098587,-0.80321,176.37
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.50691,0.81558,-0.27904,-5.7365,-0.41972,0.51628,0.74651,41.253,0.75291,-0.2613,0.60403,-31.317,#13,0.30281,0.76015,0.57488,-156.17,0.16439,0.5525,-0.81714,239.85,-0.93877,0.34194,0.042342,287.41,#7,-0.18677,-0.89987,-0.39415,197.12,0.55865,0.23274,-0.79608,172.6,0.8081,-0.36888,0.45924,233.29,#14,-0.12353,-0.99184,0.031387,185.55,-0.79976,0.080783,-0.59487,272.78,0.58748,-0.098587,-0.80321,170.49
> view matrix models
> #12,0.50691,0.81558,-0.27904,9.9167,-0.41972,0.51628,0.74651,33.521,0.75291,-0.2613,0.60403,16.781,#13,0.30281,0.76015,0.57488,-140.52,0.16439,0.5525,-0.81714,232.12,-0.93877,0.34194,0.042342,335.51,#7,-0.18677,-0.89987,-0.39415,212.77,0.55865,0.23274,-0.79608,164.87,0.8081,-0.36888,0.45924,281.39,#14,-0.12353,-0.99184,0.031387,201.2,-0.79976,0.080783,-0.59487,265.04,0.58748,-0.098587,-0.80321,218.59
> view matrix models
> #12,0.50691,0.81558,-0.27904,8.0977,-0.41972,0.51628,0.74651,18.777,0.75291,-0.2613,0.60403,10.752,#13,0.30281,0.76015,0.57488,-142.34,0.16439,0.5525,-0.81714,217.38,-0.93877,0.34194,0.042342,329.48,#7,-0.18677,-0.89987,-0.39415,210.95,0.55865,0.23274,-0.79608,150.12,0.8081,-0.36888,0.45924,275.36,#14,-0.12353,-0.99184,0.031387,199.38,-0.79976,0.080783,-0.59487,250.3,0.58748,-0.098587,-0.80321,212.56
> ui tool show "Fit in Map"
> fitmap #7 inMap #8
Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
using 6848 atoms
average map value = 0.173, steps = 260
shifted from previous position = 48.5
rotated from previous position = 29.3 degrees
atoms outside contour = 2636, contour level = 0.15
Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
(#8) coordinates:
Matrix rotation and translation
0.04300397 -0.84679709 -0.53017484 198.19738925
0.86630357 0.29594287 -0.40241266 225.13680889
0.49766333 -0.44198701 0.74631005 288.74020833
Axis -0.01980517 -0.51438666 0.85732964
Axis point -74.60302156 321.35625507 0.00000000
Rotation angle (degrees) 87.55682955
Shift along axis 127.81283363
> undo
[deleted to fit within ticket limits]
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> show #!16 models
> hide #!16 models
Drag select of 31 residues
> view sel
> ui tool show "Side View"
> select clear
> lighting simple
> lighting soft
> show #!16 models
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie7.mp4
Movie saved to /Users/szhang3/Desktop/movie7.mp4
> rock axis y
> stop
> rock axis y
> stop
> show #!12 models
> hide #!12 models
> rock axis y
> movie record
> movie encode /Users/szhang3/Desktop/movie8.mp4
Movie saved to /Users/szhang3/Desktop/movie8.mp4
> stop
> show #!12 models
> hide #!16 models
> hide #17 models
> show #17 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #17 models
> show #17 models
> hide #!14 models
> show #!14 models
> combine #14,17
Remapping chain ID 'B' in ranked_0.pdb #17 to 'F'
> rename #18 RSVA-mono_MEDI_Mota_101Fab
> hide #17 models
> hide #!14 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!12 models
> show #!18 models
> hide #!18 models
> show #!18 models
> combine #14,17
Remapping chain ID 'B' in ranked_0.pdb #17 to 'F'
> hide #!18 models
> hide #!19 models
> show #!19 models
> select #19/C:111
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 7 residues, 1 model selected
> select up
817 atoms, 833 bonds, 106 residues, 1 model selected
> select up
15037 atoms, 15330 bonds, 1738 residues, 1 model selected
> select down
817 atoms, 833 bonds, 106 residues, 1 model selected
> select up
15037 atoms, 15330 bonds, 1738 residues, 1 model selected
> select down
817 atoms, 833 bonds, 106 residues, 1 model selected
> select clear
Drag select of 108 residues, 1 pseudobonds
> select up
1154 atoms, 1174 bonds, 1 pseudobond, 154 residues, 2 models selected
> select up
1491 atoms, 1525 bonds, 1 pseudobond, 198 residues, 2 models selected
> delete atoms (#!19 & sel)
> delete bonds (#!19 & sel)
> rename #19 RSVA-mono_MEDI_Mota_101Fv
> show #!16 models
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/101/RSVA-
> mono_MEDI_Mota_101Fab.pdb" models #18 relModel #16
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/101/RSVA-
> mono_MEDI_Mota_101Fv.pdb" models #19 relModel #16
> close #17
> close #14
> show #!18 models
> hide #!19 models
> hide #!16 models
> show #!12 models
> hide #!18 models
> select #12/B:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 5 residues, 1 model selected
> select up
3482 atoms, 3540 bonds, 449 residues, 1 model selected
> show #!18 models
> hide #!18 models
> color sel hot pink
> select #12/C:433
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> select up
3482 atoms, 3541 bonds, 449 residues, 1 model selected
> color sel light gray
> select clear
> show #!18 models
> undo
> select clear
> show #!18 models
> rock axis y
> show #!16 models
> stop
> hide #18.1 models
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie7.mp4
Movie saved to /Users/szhang3/Desktop/movie7.mp4
> hide #!12 models
> show #!12 models
> rock axis y
> stop
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie8.mp4
Movie saved to /Users/szhang3/Desktop/movie8.mp4
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!1 models
> hide #!1 models
> hide #!12 models
> hide #!16 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie9.mp4
Movie saved to /Users/szhang3/Desktop/movie9.mp4
Drag select of 23 residues
> view sel
> ui tool show "Side View"
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie10.mp4
Movie saved to /Users/szhang3/Desktop/movie10.mp4
> open /Users/szhang3/Downloads/cryosparc_P141_J34_002_volume_map_sharp.mrc
Opened cryosparc_P141_J34_002_volume_map_sharp.mrc as #14, grid size
208,208,208, pixel 2, shown at level 0.135, step 1, values float32
> close #14
> show #!15 models
> hide #!18 models
> show #!16 models
> hide #!16 models
> show #!13 models
Drag select of 263 residues, 15 cryosparc_P141_J36_001_volume_map.mrc
> hide #!15 models
> select up
2371 atoms, 2420 bonds, 311 residues, 3 models selected
> select up
3237 atoms, 3321 bonds, 424 residues, 3 models selected
> select subtract #15
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #8671ffff
> color sel #b146ffff
> select clear
Drag select of 306 residues, 1 pseudobonds
Drag select of 301 residues
Drag select of 135 residues
> select up
7076 atoms, 7228 bonds, 1 pseudobond, 939 residues, 2 models selected
> select up
9711 atoms, 9963 bonds, 1 pseudobond, 1272 residues, 2 models selected
> select up
20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 2 models selected
> select down
9711 atoms, 9963 bonds, 1 pseudobond, 1272 residues, 2 models selected
> color (#!13 & sel) #8671ffff
> select clear
> hide #13.1 models
> select clear
Cell requested for row 13 is out of bounds for table with 18 rows! Resizing
table model.
> show #!15 models
> rename #15 cryosparc_P141_J36_001_volume_map_102.mrc
> hide #!13 models
> show #!13 models
> hide #!15 models
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/102/AF2_102/102mab/ranked_0.pdb
Chain information for ranked_0.pdb #14
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select add #14
3303 atoms, 3347 bonds, 222 residues, 1 model selected
Drag select of 197 residues
> select up
5234 atoms, 5317 bonds, 480 residues, 2 models selected
> select up
6540 atoms, 6668 bonds, 646 residues, 2 models selected
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/102/AF2_102/102mab/ranked_0.pdb
Chain information for ranked_0.pdb #17
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/102/AF2_102/102mab/ranked_0.pdb
Chain information for ranked_0.pdb #20
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select add #17
9843 atoms, 10015 bonds, 868 residues, 3 models selected
> select add #20
13146 atoms, 13362 bonds, 1090 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #14 to #13
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 102_RSVA-PreF-trimer.pdb, chain D (#13) with ranked_0.pdb, chain A
(#14), sequence alignment score = 258.8
RMSD between 100 pruned atom pairs is 0.927 angstroms; (across all 114 pairs:
2.093)
> hide #17 models
> select subtract #17
9843 atoms, 10015 bonds, 868 residues, 3 models selected
> select add #17
13146 atoms, 13362 bonds, 1090 residues, 4 models selected
> show #17 models
> hide #14 models
> select subtract #14
9843 atoms, 10015 bonds, 868 residues, 3 models selected
> select clear
Drag select of 92 residues
> select up
1440 atoms, 1467 bonds, 190 residues, 1 model selected
> select up
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> select add #17
6540 atoms, 6668 bonds, 646 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #17 & sel to #13 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 102_RSVA-PreF-trimer.pdb, chain M (#13) with ranked_0.pdb, chain A
(#17), sequence alignment score = 258.8
RMSD between 100 pruned atom pairs is 0.927 angstroms; (across all 114 pairs:
2.093)
> select clear
Drag select of 145 residues
> select up
1654 atoms, 1692 bonds, 216 residues, 1 model selected
> select up
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> select add #20
6540 atoms, 6668 bonds, 646 residues, 2 models selected
> matchmaker #20 & sel to #13 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 102_RSVA-PreF-trimer.pdb, chain G (#13) with ranked_0.pdb, chain A
(#20), sequence alignment score = 258.8
RMSD between 100 pruned atom pairs is 0.927 angstroms; (across all 114 pairs:
2.093)
> show #14 models
> select clear
> hide #17 models
> hide #20 models
> hide #14 models
Drag select of 124 residues
Drag select of 167 residues
Drag select of 184 residues
> select up
2061 atoms, 2106 bonds, 273 residues, 1 model selected
> select up
3237 atoms, 3321 bonds, 424 residues, 1 model selected
Drag select of 269 residues
Drag select of 138 residues
> select up
7055 atoms, 7219 bonds, 934 residues, 1 model selected
> select up
9711 atoms, 9963 bonds, 1272 residues, 1 model selected
> select up
20544 atoms, 20995 bonds, 2658 residues, 1 model selected
> select down
9711 atoms, 9963 bonds, 1272 residues, 1 model selected
> select up
20544 atoms, 20995 bonds, 2658 residues, 1 model selected
> select down
9711 atoms, 9963 bonds, 1272 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #9193cfff
> select clear
Drag select of 145 residues
> select add #13/R:108
1118 atoms, 10 bonds, 146 residues, 1 model selected
> select add #13/D:113
1124 atoms, 15 bonds, 147 residues, 1 model selected
> select add #13/R:109
1131 atoms, 21 bonds, 148 residues, 1 model selected
Drag select of 40 residues
> delete atoms sel
> delete bonds sel
> select #13/D:59
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 3 residues, 1 model selected
> select up
120 atoms, 126 bonds, 13 residues, 1 model selected
> select up
129 atoms, 134 bonds, 14 residues, 1 model selected
> select add #13/D:35
135 atoms, 139 bonds, 15 residues, 1 model selected
> select add #13/D:95
143 atoms, 146 bonds, 16 residues, 1 model selected
> select add #13/R:54
151 atoms, 153 bonds, 17 residues, 1 model selected
> select up
182 atoms, 184 bonds, 21 residues, 1 model selected
> select up
233 atoms, 236 bonds, 29 residues, 1 model selected
> select add #13/D:72
241 atoms, 243 bonds, 30 residues, 1 model selected
> select up
264 atoms, 266 bonds, 33 residues, 1 model selected
> select up
294 atoms, 296 bonds, 37 residues, 1 model selected
> select up
1795 atoms, 1831 bonds, 236 residues, 1 model selected
> select down
294 atoms, 296 bonds, 37 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 179 residues
> select up
1653 atoms, 1691 bonds, 218 residues, 1 model selected
> select add #13/G:58
1663 atoms, 1701 bonds, 219 residues, 1 model selected
> select up
1684 atoms, 1724 bonds, 221 residues, 1 model selected
> select up
2653 atoms, 2722 bonds, 345 residues, 1 model selected
> select down
1684 atoms, 1724 bonds, 221 residues, 1 model selected
Drag select of 19 residues
Drag select of 36 residues
> select subtract #13/G:141
1805 atoms, 1724 bonds, 237 residues, 1 model selected
> select subtract #13/G:121
1798 atoms, 1724 bonds, 236 residues, 1 model selected
> select subtract #13/G:208
1790 atoms, 1724 bonds, 235 residues, 1 model selected
> select subtract #13/G:196
1784 atoms, 1724 bonds, 234 residues, 1 model selected
> select subtract #13/G:155
1776 atoms, 1724 bonds, 233 residues, 1 model selected
> select add #13/G:141
1784 atoms, 1731 bonds, 234 residues, 1 model selected
> select subtract #13/G:142
1777 atoms, 1731 bonds, 233 residues, 1 model selected
> select subtract #13/G:141
1769 atoms, 1724 bonds, 232 residues, 1 model selected
> select subtract #13/G:143
1760 atoms, 1724 bonds, 231 residues, 1 model selected
> select subtract #13/G:152
1753 atoms, 1724 bonds, 230 residues, 1 model selected
> select subtract #13/G:150
1746 atoms, 1724 bonds, 229 residues, 1 model selected
> select clear
Drag select of 170 residues
> delete atoms sel
> delete bonds sel
Drag select of 17 residues
> delete atoms sel
> delete bonds sel
> select #13/G:58
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #13/E:1
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #13/E:94
30 atoms, 29 bonds, 3 residues, 1 model selected
> select add #13/E:29
41 atoms, 39 bonds, 4 residues, 1 model selected
> select add #13/G:64
50 atoms, 47 bonds, 5 residues, 1 model selected
> select up
193 atoms, 192 bonds, 26 residues, 1 model selected
> select up
1079 atoms, 1100 bonds, 138 residues, 1 model selected
> select down
193 atoms, 192 bonds, 26 residues, 1 model selected
> select down
50 atoms, 47 bonds, 5 residues, 1 model selected
> select add #13/G:51
58 atoms, 54 bonds, 6 residues, 1 model selected
> select add #13/G:69
66 atoms, 61 bonds, 7 residues, 1 model selected
> select up
244 atoms, 243 bonds, 32 residues, 1 model selected
> select down
66 atoms, 61 bonds, 7 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 7 residues
> select add #13/G:60
63 atoms, 7 bonds, 8 residues, 1 model selected
> select add #13/E:26
69 atoms, 12 bonds, 9 residues, 1 model selected
> select add #13/E:27
75 atoms, 17 bonds, 10 residues, 1 model selected
> select add #13/G:59
87 atoms, 29 bonds, 11 residues, 1 model selected
> select add #13/G:57
96 atoms, 37 bonds, 12 residues, 1 model selected
> select add #13/G:53
110 atoms, 52 bonds, 13 residues, 1 model selected
> select add #13/G:31
117 atoms, 58 bonds, 14 residues, 1 model selected
> select up
252 atoms, 246 bonds, 35 residues, 1 model selected
> select down
117 atoms, 58 bonds, 14 residues, 1 model selected
> select add #13/G:52
131 atoms, 73 bonds, 15 residues, 1 model selected
> select add #13/G:55
139 atoms, 80 bonds, 16 residues, 1 model selected
> select add #13/G:56
148 atoms, 88 bonds, 17 residues, 1 model selected
> select add #13/G:97
156 atoms, 95 bonds, 18 residues, 1 model selected
> select add #13/G:32
161 atoms, 99 bonds, 19 residues, 1 model selected
> select add #13/G:33
165 atoms, 102 bonds, 20 residues, 1 model selected
> select add #13/G:54
173 atoms, 109 bonds, 21 residues, 1 model selected
> select add #13/G:30
179 atoms, 114 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #13/E:31
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #13/E:30
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #13/E:69
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #13/E:68
22 atoms, 18 bonds, 4 residues, 1 model selected
> select add #13/G:99
30 atoms, 25 bonds, 5 residues, 1 model selected
> select add #13/G:98
41 atoms, 36 bonds, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #13/E:93
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #13/E:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #13/E:93
10 atoms, 8 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 111 residues
> select clear
Drag select of 143 residues
> select clear
Drag select of 163 residues
> select clear
Drag select of 200 residues
> select up
1698 atoms, 1737 bonds, 221 residues, 1 model selected
> select down
1542 atoms, 200 residues, 1 model selected
> select add #13/L:67
1548 atoms, 5 bonds, 201 residues, 1 model selected
> select add #13/L:69
1555 atoms, 11 bonds, 202 residues, 1 model selected
> select add #13/L:68
1559 atoms, 14 bonds, 203 residues, 1 model selected
> select add #13/L:32
1571 atoms, 26 bonds, 204 residues, 1 model selected
> select add #13/L:31
1575 atoms, 29 bonds, 205 residues, 1 model selected
> select add #13/M:98
1586 atoms, 40 bonds, 206 residues, 1 model selected
> select add #13/L:92
1592 atoms, 45 bonds, 207 residues, 1 model selected
> select add #13/L:27
1598 atoms, 50 bonds, 208 residues, 1 model selected
> select add #13/L:29
1609 atoms, 60 bonds, 209 residues, 1 model selected
> select add #13/L:30
1616 atoms, 66 bonds, 210 residues, 1 model selected
> select add #13/M:99
1624 atoms, 73 bonds, 211 residues, 1 model selected
> select add #13/M:97
1632 atoms, 80 bonds, 212 residues, 1 model selected
> select add #13/L:93
1636 atoms, 83 bonds, 213 residues, 1 model selected
> select add #13/L:94
1648 atoms, 95 bonds, 214 residues, 1 model selected
> select add #13/L:1
1656 atoms, 102 bonds, 215 residues, 1 model selected
> select add #13/L:2
1664 atoms, 109 bonds, 216 residues, 1 model selected
> select add #13/M:53
1678 atoms, 124 bonds, 217 residues, 1 model selected
> select add #13/M:54
1686 atoms, 131 bonds, 218 residues, 1 model selected
> select add #13/M:55
1694 atoms, 138 bonds, 219 residues, 1 model selected
> select add #13/M:57
1703 atoms, 146 bonds, 220 residues, 1 model selected
> select add #13/M:56
1712 atoms, 154 bonds, 221 residues, 1 model selected
> select add #13/M:52
1726 atoms, 169 bonds, 222 residues, 1 model selected
> select add #13/M:32
1731 atoms, 173 bonds, 223 residues, 1 model selected
> select add #13/M:33
1735 atoms, 176 bonds, 224 residues, 1 model selected
> select add #13/M:31
1742 atoms, 182 bonds, 225 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #14 models
> show #17 models
> show #20 models
> color #14 #8671ffff
> color #17 #8671ffff
> color #20 #8671ffff
> show #!15 models
> select add #14
3303 atoms, 3347 bonds, 222 residues, 1 model selected
> select add #17
6606 atoms, 6694 bonds, 444 residues, 2 models selected
> select add #20
9909 atoms, 10041 bonds, 666 residues, 3 models selected
> hide #!13 models
> show #!13 models
> fitmap #14 inMap #15
Fit molecule ranked_0.pdb (#14) to map
cryosparc_P141_J36_001_volume_map_102.mrc (#15) using 3303 atoms
average map value = 2.79, steps = 224
shifted from previous position = 52.8
rotated from previous position = 56.5 degrees
atoms outside contour = 0, contour level = 1.0438
Position of ranked_0.pdb (#14) relative to
cryosparc_P141_J36_001_volume_map_102.mrc (#15) coordinates:
Matrix rotation and translation
-0.62734549 0.77176533 -0.10399957 217.72604797
0.69329175 0.49268381 -0.52593651 226.86042132
-0.35466065 -0.40204594 -0.84414151 228.48561977
Axis 0.42660575 0.86312836 -0.27021653
Axis point 65.05331663 0.00000000 144.64183947
Rotation angle (degrees) 171.65085044
Shift along axis 226.95225413
> undo
> color #20 #8671ffff
> select add #14
3303 atoms, 3347 bonds, 222 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.62735,0.77177,-0.104,177.43,0.69329,0.49268,-0.52594,222.68,-0.35466,-0.40205,-0.84414,254.73
> view matrix models
> #14,-0.62735,0.77177,-0.104,181.89,0.69329,0.49268,-0.52594,226.92,-0.35466,-0.40205,-0.84414,256.74
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.71871,0.19046,0.66872,185.79,0.59691,0.66225,0.45292,228.69,-0.3566,0.72468,-0.58965,253.42
> view matrix models
> #14,-0.44435,-0.76836,0.46062,188.81,0.14195,-0.56806,-0.81065,229.59,0.88453,-0.29483,0.36149,260.14
> view matrix models
> #14,-0.55212,-0.79977,0.23565,188.29,0.05904,-0.31943,-0.94577,228.33,0.83167,-0.50827,0.22358,260.52
> show #!15 models
> view matrix models
> #14,-0.55504,-0.7989,0.23173,188.28,0.058002,-0.31507,-0.9473,228.31,0.8298,-0.51234,0.22121,260.52
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.55504,-0.7989,0.23173,179.05,0.058002,-0.31507,-0.9473,218.94,0.8298,-0.51234,0.22121,256.5
> view matrix models
> #14,-0.55504,-0.7989,0.23173,178.89,0.058002,-0.31507,-0.9473,220.15,0.8298,-0.51234,0.22121,260.29
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.63621,-0.77016,0.045735,178.28,0.60285,-0.53324,-0.59349,222.14,0.48147,-0.35001,0.80354,260.94
> view matrix models
> #14,-0.52502,-0.69318,-0.49381,176.74,0.56671,0.14815,-0.81049,219.19,0.63498,-0.70537,0.31505,261.07
> hide #!15 models
> show #!15 models
> view matrix models
> #14,-0.46607,-0.69123,-0.55224,176.63,-0.18176,0.68567,-0.70485,217.09,0.86588,-0.22813,-0.44521,257.66
> hide #!15 models
> view matrix models
> #14,0.63032,-0.46315,-0.62306,176.35,0.43449,-0.45465,0.77751,225.15,-0.64337,-0.76078,-0.08534,259.46
> view matrix models
> #14,-0.82198,-0.12488,0.55566,177.16,0.29305,-0.92934,0.22463,225.36,0.48834,0.34748,0.80049,258.49
> delete atoms sel
> delete bonds sel
> hide #17 models
> show #17 models
> hide #20 models
> show #20 models
> combine #13,17,20
Remapping chain ID 'A' in ranked_0.pdb #17 to 'S'
Remapping chain ID 'B' in ranked_0.pdb #17 to 'T'
Remapping chain ID 'A' in ranked_0.pdb #20 to 'U'
Remapping chain ID 'B' in ranked_0.pdb #20 to 'V'
> hide #!13 models
> hide #17 models
> hide #20 models
> rename #14 RSVA-trimer_102Fab
> show #!15 models
> hide #!15 models
> show #!15 models
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/RSVA-trimer_102Fab.pdb"
> models #14 relModel #15
> open /Users/szhang3/Library/CloudStorage/OneDrive-Moderna/RSV/MAbs/102/RSVA-
> trimer_102Fab.pdb
Chain information for RSVA-trimer_102Fab.pdb #21
---
Chain | Description
A B C | No description available
D G M | No description available
E L R | No description available
S U | No description available
T V | No description available
> hide #!15 models
> hide #!14 models
> select #21/K:601@CL
1 atom, 1 residue, 1 model selected
> select add #21/P:601@CL
2 atoms, 2 residues, 1 model selected
> select add #21/Q:601@CL
3 atoms, 3 residues, 1 model selected
Drag select of 105 atoms
> select up
130 atoms, 137 bonds, 14 residues, 1 model selected
Drag select of 19 atoms
> select up
180 atoms, 189 bonds, 18 residues, 1 model selected
> select up
257 atoms, 274 bonds, 25 residues, 1 model selected
Drag select of 2 atoms
> select up
275 atoms, 291 bonds, 27 residues, 1 model selected
> select up
299 atoms, 315 bonds, 31 residues, 1 model selected
> select down
275 atoms, 291 bonds, 27 residues, 1 model selected
> select add #21/D:100B@CD1
276 atoms, 291 bonds, 28 residues, 1 model selected
> select up
286 atoms, 302 bonds, 28 residues, 1 model selected
> select up
310 atoms, 326 bonds, 32 residues, 1 model selected
> select down
286 atoms, 302 bonds, 28 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 47 atoms
> select up
69 atoms, 73 bonds, 6 residues, 1 model selected
> select up
127 atoms, 137 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #21/H:612@CL
1 atom, 1 residue, 1 model selected
> select up
21528 atoms, 21889 bonds, 2389 residues, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> view matrix models
> #21,0.98978,0.13978,0.028083,-32.582,-0.14096,0.98897,0.04541,23.889,-0.021426,-0.048905,0.99857,15.159
> delete atoms sel
> delete bonds sel
> select clear
> hide #!21 atoms
> show #!21 cartoons
> show #!14 models
> hide #!14 models
> show #!14 models
> select add #21
21527 atoms, 21889 bonds, 12 pseudobonds, 2388 residues, 2 models selected
> view matrix models
> #21,-0.3201,0.25008,0.91378,44.277,0.46934,0.87971,-0.076349,-63.042,-0.82296,0.40444,-0.39897,403.01
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.3201,0.25008,0.91378,21.326,0.46934,0.87971,-0.076349,-54.994,-0.82296,0.40444,-0.39897,406.61
> view matrix models
> #21,-0.3201,0.25008,0.91378,23.366,0.46934,0.87971,-0.076349,-55.404,-0.82296,0.40444,-0.39897,404.25
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.4491,0.29211,0.84439,58.458,0.50475,0.86274,-0.029997,-69.835,-0.73725,0.41274,-0.5349,412.93
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.4491,0.29211,0.84439,58,0.50475,0.86274,-0.029997,-69.2,-0.73725,0.41274,-0.5349,409.84
> ui tool show Matchmaker
> matchmaker #!21 & sel to #14 & sel
No 'to' model specified
> select clear
Drag select of 65 residues
> select up
1104 atoms, 1104 bonds, 138 residues, 2 models selected
> select up
20870 atoms, 21218 bonds, 2692 residues, 2 models selected
> matchmaker #!21 & sel to #14 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RSVA-trimer_102Fab, chain A (#14) with RSVA-trimer_102Fab.pdb,
chain A (#21), sequence alignment score = 2486.8
RMSD between 448 pruned atom pairs is 0.000 angstroms; (across all 448 pairs:
0.000)
> select clear
> select add #21
21527 atoms, 21889 bonds, 12 pseudobonds, 2388 residues, 2 models selected
> view matrix models
> #21,1,1.8341e-07,-9.4532e-07,-2.8853,-1.8368e-07,1,2.7799e-07,0.66478,9.4473e-07,-2.7833e-07,1,0.7915
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.13032,0.21959,0.96685,-64.28,0.59565,0.76223,-0.2534,-27.871,-0.7926,0.60892,-0.03147,275.08
> view matrix models
> #21,0.10785,0.24986,0.96226,-64.54,0.53875,0.79877,-0.26779,-19.636,-0.83553,0.5473,-0.048461,301.08
> view matrix models
> #21,-0.095715,0.37139,0.92353,-35.936,0.63736,0.73553,-0.22973,-36.773,-0.7646,0.56663,-0.30711,337.37
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.095715,0.37139,0.92353,-46.259,0.63736,0.73553,-0.22973,-29.312,-0.7646,0.56663,-0.30711,343.36
> select clear
> select #14/C:510
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #21/B:507
19 atoms, 17 bonds, 2 residues, 2 models selected
> select up
352 atoms, 352 bonds, 44 residues, 2 models selected
> select up
6964 atoms, 7081 bonds, 898 residues, 2 models selected
> matchmaker #!21 & sel to #14 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RSVA-trimer_102Fab, chain C (#14) with RSVA-trimer_102Fab.pdb,
chain B (#21), sequence alignment score = 2483.2
RMSD between 438 pruned atom pairs is 0.403 angstroms; (across all 449 pairs:
0.722)
> select clear
> select #21/U:4
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #21/V:45
29 atoms, 27 bonds, 2 residues, 1 model selected
> select up
130 atoms, 128 bonds, 8 residues, 1 model selected
> select up
3303 atoms, 3347 bonds, 222 residues, 1 model selected
> select ~sel & ##selected
18224 atoms, 18542 bonds, 12 pseudobonds, 2166 residues, 2 models selected
> delete atoms (#!21 & sel)
> delete bonds (#!21 & sel)
> select clear
> select ~sel & ##selected
Nothing selected
> combine #14,21
Remapping chain ID 'U' in RSVA-trimer_102Fab.pdb #21 to 'W'
Remapping chain ID 'V' in RSVA-trimer_102Fab.pdb #21 to 'X'
> hide #!21 models
> hide #!14 models
> close #21
> show #!13 models
> hide #!13 models
> close #13
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/RSVA-trimer_102Fab.pdb"
> models #22 relModel #15
> open /Users/szhang3/Library/CloudStorage/OneDrive-Moderna/RSV/MAbs/102/RSVA-
> trimer_102Fab.pdb
Chain information for RSVA-trimer_102Fab.pdb #13
---
Chain | Description
A B C | No description available
D G M | No description available
E L R | No description available
S U W | No description available
T V X | No description available
> hide #!13,22 atoms
> show #!13,22 cartoons
> show #!13,22 atoms
> close #22
Drag select of 76 atoms
> select up
99 atoms, 107 bonds, 9 residues, 1 model selected
> select up
127 atoms, 137 bonds, 11 residues, 1 model selected
> select add #13/Q:601@CL
128 atoms, 137 bonds, 12 residues, 1 model selected
> select add #13/P:601@CL
129 atoms, 137 bonds, 13 residues, 1 model selected
> select add #13/K:601@CL
130 atoms, 137 bonds, 14 residues, 1 model selected
> select add #13/O:4@C4
131 atoms, 137 bonds, 15 residues, 1 model selected
> select up
141 atoms, 148 bonds, 15 residues, 1 model selected
> select up
257 atoms, 274 bonds, 25 residues, 1 model selected
> select add #13/I:3@O2
258 atoms, 274 bonds, 26 residues, 1 model selected
> select up
268 atoms, 285 bonds, 26 residues, 1 model selected
> select up
384 atoms, 411 bonds, 36 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/RSVA-trimer_102Fab.pdb"
> models #13 relModel #15
> open /Users/szhang3/Library/CloudStorage/OneDrive-Moderna/RSV/MAbs/102/RSVA-
> trimer_102Fab.pdb
Chain information for RSVA-trimer_102Fab.pdb #21
---
Chain | Description
A B C | No description available
D G M | No description available
E L R | No description available
S U W | No description available
T V X | No description available
> close #21
> hide #!13 atoms
> show #!13 cartoons
> hide #13.1 models
Drag select of 118 residues
> select up
1797 atoms, 1808 bonds, 223 residues, 1 model selected
> select up
10435 atoms, 10609 bonds, 1346 residues, 1 model selected
> color sel gray
> color sel light gray
> select clear
> select #13/T:18
10 atoms, 9 bonds, 1 residue, 1 model selected
Drag select of 54 residues
Drag select of 76 residues
Drag select of 91 residues
> select up
3398 atoms, 3409 bonds, 221 residues, 1 model selected
> select up
5862 atoms, 5928 bonds, 390 residues, 1 model selected
> select up
9909 atoms, 10041 bonds, 666 residues, 1 model selected
> select up
24860 atoms, 25264 bonds, 2614 residues, 1 model selected
> select down
9909 atoms, 10041 bonds, 666 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #a392b7ff
> color sel #8671ffff
> select clear
Drag select of 43 residues
Drag select of 160 residues
Drag select of 52 residues
> select up
2665 atoms, 2705 bonds, 357 residues, 1 model selected
> select up
4460 atoms, 4563 bonds, 593 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #9193cfff
> select clear
> show #!15 models
> volume #15 level 1.199
> hide #!15 models
> transparency 50
> show #!15 models
Cell requested for row 14 is out of bounds for table with 21 rows! Resizing
table model.
> set bgColor white
> lighting simple
> lighting soft
> color #15 #ead0e680 models
> select clear
> hide #!15 models
> show #!15 models
> volume #15 level 1.035
> hide #!15 models
Drag select of 55 residues
> select #13/A:45
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/A:52
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #13/B:152
29 atoms, 28 bonds, 3 residues, 1 model selected
> view sel
> view matrix models #13,1,0,0,-3.4945,0,1,0,-7.729,0,0,1,-1.8359
> view matrix models #13,1,0,0,-10.809,0,1,0,-24.954,0,0,1,-5.549
> ui mousemode right zoom
> undo
> select add #13/B:153
27 atoms, 26 bonds, 3 residues, 1 model selected
> view sel
> ui tool show "Side View"
> select clear
> select #13/A:44
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 11 residues, 1 model selected
> select up
3471 atoms, 3528 bonds, 448 residues, 1 model selected
> color sel gray
> select clear
> show #!15 models
> rock axis y
> movie record
> movie encode /Users/szhang3/Desktop/movie7.mp4
Movie saved to /Users/szhang3/Desktop/movie7.mp4
> stop
> hide #!15 models
> show #!5 models
> show #!15 models
> hide #!15 models
> hide #!5 models
> show #!1 models
> select #13/A:205
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 6 residues, 1 model selected
> select up
3471 atoms, 3528 bonds, 448 residues, 1 model selected
> color sel light gray
> select #13/B:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 5 residues, 1 model selected
> select up
3482 atoms, 3540 bonds, 449 residues, 1 model selected
> color sel gray
> select clear
Drag select of 81 residues
> select up
1225 atoms, 1241 bonds, 146 residues, 1 model selected
> select up
3052 atoms, 3106 bonds, 306 residues, 1 model selected
> select add #13/U:6
3069 atoms, 3122 bonds, 307 residues, 1 model selected
> select add #13/U:29
3089 atoms, 3142 bonds, 308 residues, 1 model selected
> select up
3172 atoms, 3225 bonds, 313 residues, 1 model selected
> select up
4803 atoms, 4881 bonds, 421 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> select up
4809 atoms, 4886 bonds, 422 residues, 1 model selected
> select up
24860 atoms, 25264 bonds, 2614 residues, 1 model selected
> select up
99284 atoms, 101033 bonds, 11001 residues, 32 models selected
> select up
99284 atoms, 101033 bonds, 11001 residues, 32 models selected
> rock axis y
> select clear
> movie record
> movie encode /Users/szhang3/Desktop/movie8.mp4
Movie saved to /Users/szhang3/Desktop/movie8.mp4
> stop
===== 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 - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 8 days, 1 hour, 38 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LS34A650U:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
narwhals: 1.31.0
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: 2.2.4
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
plotly: 6.0.1
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
pyKVFinder: 0.7.3
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
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 months 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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