![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Last modified 6 months ago
#18023 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-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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"codeSigningMonitor" : 1,
"incident" : "43B799FC-6148-4B3E-91E9-C7EA32BFFF10",
"pid" : 31637,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
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"procLaunch" : "2025-06-18 08:04:32.2607 -0400",
"procStartAbsTime" : 2690059162070,
"procExitAbsTime" : 2812188656149,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31637},
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"arch" : "arm64",
"base" : 6097993728,
"size" : 32768,
"uuid" : "93fd54d8-5d5e-319d-94c5-2702d533d751",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6589030400,
"size" : 241656,
"uuid" : "eee9d0d3-dffc-37cb-9ced-b27cd0286d8c",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6589272064,
"size" : 53248,
"uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6587805696,
"size" : 532476,
"uuid" : "92699527-645f-3d8d-aed8-1cfb0c034e15",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6589509632,
"size" : 32748,
"uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6652358656,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21221376,
"uuid" : "b88a44c1-d617-33dc-90ed-b6ab417c428e",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.40.6"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6685978624,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5427200,
"uuid" : "f66e0c94-99b5-3fcd-b726-3e3cbca668a3",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6587502592,
"size" : 290816,
"uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6589739008,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5197824,
"uuid" : "190e6a36-fcaa-3ea3-94bb-7009c44653da",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3302.1.400"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6779396096,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3178496,
"uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6585606144,
"size" : 532288,
"uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6608556032,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14974976,
"uuid" : "16d282d0-8b48-3e76-8036-fcb45dece518",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3302.1.400"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6586138624,
"size" : 16377,
"uuid" : "a33d811c-bd2d-3833-9c38-9bf3960a1f8c",
"path" : "\/usr\/lib\/system\/libsystem_blocks.dylib",
"name" : "libsystem_blocks.dylib"
}
],
"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" : [
{
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"factorPackIds" : {
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{
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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
> fitmap #14 inMap #8
Fit molecule 4zyp_Mota_AM14.pdb (#14) to map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 29990 atoms
average map value = 0.08896, steps = 100
shifted from previous position = 20.1
rotated from previous position = 10 degrees
atoms outside contour = 20375, contour level = 0.15
Position of 4zyp_Mota_AM14.pdb (#14) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
-0.17692084 -0.98261169 0.05633196 201.63862391
-0.69014872 0.08304951 -0.71888631 243.27619117
0.70170775 -0.16606341 -0.69284138 205.86393215
Axis 0.61513774 -0.71812328 0.32542973
Axis point 171.87387039 0.00000000 189.71400218
Rotation angle (degrees) 153.29808359
Shift along axis 16.32747378
> select subtract #14
6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 6 models selected
> view matrix models
> #12,0.50691,0.81558,-0.27904,12.765,-0.41972,0.51628,0.74651,11.36,0.75291,-0.2613,0.60403,18.138,#13,0.30281,0.76015,0.57488,-137.67,0.16439,0.5525,-0.81714,209.96,-0.93877,0.34194,0.042342,336.86,#7,-0.18677,-0.89987,-0.39415,215.62,0.55865,0.23274,-0.79608,142.71,0.8081,-0.36888,0.45924,282.74
> view matrix models
> #12,0.50691,0.81558,-0.27904,20.376,-0.41972,0.51628,0.74651,11.812,0.75291,-0.2613,0.60403,7.1867,#13,0.30281,0.76015,0.57488,-130.06,0.16439,0.5525,-0.81714,210.41,-0.93877,0.34194,0.042342,325.91,#7,-0.18677,-0.89987,-0.39415,223.23,0.55865,0.23274,-0.79608,143.16,0.8081,-0.36888,0.45924,271.79
> 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 = 284
shifted from previous position = 59.9
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
0.04241308 -0.84625872 -0.53108127 198.12554067
0.86642041 0.29584870 -0.40223031 225.15960097
0.49751061 -0.44307982 0.74576368 288.72808585
Axis -0.02044280 -0.51475043 0.85709631
Axis point -74.41913812 321.40895395 0.00000000
Rotation angle (degrees) 87.59213926
Shift along axis 127.51653607
> view matrix models
> #12,0.50691,0.81558,-0.27904,25.841,-0.41972,0.51628,0.74651,-41.303,0.75291,-0.2613,0.60403,13.675,#13,0.30281,0.76015,0.57488,-124.6,0.16439,0.5525,-0.81714,157.3,-0.93877,0.34194,0.042342,332.4,#7,0.042413,-0.84626,-0.53108,203.59,0.86642,0.29585,-0.40223,172.04,0.49751,-0.44308,0.74576,295.22
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.47771,0.64673,-0.59459,142.06,-0.32213,0.75862,0.56633,-64.377,0.81733,-0.079004,0.57073,-26.896,#13,0.3904,0.482,0.78439,-114.03,0.33881,0.71699,-0.60921,48.031,-0.85604,0.50359,0.11661,265.41,#7,-0.31314,-0.80892,-0.49759,194.68,0.78631,0.073003,-0.61351,163.3,0.5326,-0.58337,0.61319,292.12
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.47771,0.64673,-0.59459,150.75,-0.32213,0.75862,0.56633,-63.598,0.81733,-0.079004,0.57073,-27.684,#13,0.3904,0.482,0.78439,-105.35,0.33881,0.71699,-0.60921,48.81,-0.85604,0.50359,0.11661,264.62,#7,-0.31314,-0.80892,-0.49759,203.37,0.78631,0.073003,-0.61351,164.08,0.5326,-0.58337,0.61319,291.33
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.41314,0.61482,-0.6718,186.89,-0.39034,0.78605,0.47933,-36.78,0.82277,0.064202,0.56473,-56.837,#13,0.453,0.39802,0.79773,-100.64,0.44309,0.67595,-0.58887,34.012,-0.7736,0.62022,0.12985,218.79,#7,-0.39869,-0.75282,-0.52374,198.4,0.71237,0.10545,-0.69384,157.05,0.57757,-0.64973,0.49424,287.66
> 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 = 240
shifted from previous position = 54.9
rotated from previous position = 27.8 degrees
atoms outside contour = 2637, 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
0.04211163 -0.84599024 -0.53153282 198.08913708
0.86645607 0.29581680 -0.40217695 225.16757438
0.49747411 -0.44361351 0.74547070 288.72456108
Axis -0.02073631 -0.51495137 0.85696855
Axis point -74.33279639 321.43732765 0.00000000
Rotation angle (degrees) 87.61009779
Shift along axis 127.36987785
> undo
> select clear
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!10 models
> select #7/F:75
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #14/C:198
21 atoms, 20 bonds, 2 residues, 2 models selected
> select up
292 atoms, 292 bonds, 35 residues, 2 models selected
> select up
6964 atoms, 7081 bonds, 898 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!7 & sel to #14 & 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 4zyp_Mota_AM14.pdb, chain C (#14) with 5udc.pdb, chain F (#7),
sequence alignment score = 2359
RMSD between 436 pruned atom pairs is 0.589 angstroms; (across all 448 pairs:
1.048)
> show #!8 models
> hide #!2 models
> show #!2 models
Drag select of 172 residues, 1 pseudobonds
> select clear
Drag select of 252 residues, 1 pseudobonds
Drag select of 215 residues
Drag select of 198 residues
> select up
6378 atoms, 6495 bonds, 1 pseudobond, 848 residues, 2 models selected
> select up
9793 atoms, 10037 bonds, 1 pseudobond, 1282 residues, 2 models selected
> select up
29990 atoms, 30657 bonds, 9 pseudobonds, 3906 residues, 2 models selected
> select down
9793 atoms, 10037 bonds, 1 pseudobond, 1282 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
Drag select of 77 residues
> select up
926 atoms, 934 bonds, 125 residues, 1 model selected
> select up
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> select up
20197 atoms, 20620 bonds, 2624 residues, 1 model selected
> select down
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!14 models
> show #!14 models
> hide #!8 models
> hide #!2 models
Drag select of 7 residues
Drag select of 257 residues
> select up
2341 atoms, 2396 bonds, 305 residues, 1 model selected
> select up
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> color sel yellow
Drag select of 276 residues, 1 pseudobonds
> select up
2310 atoms, 2356 bonds, 1 pseudobond, 305 residues, 2 models selected
> select up
3237 atoms, 3313 bonds, 1 pseudobond, 428 residues, 2 models selected
> color (#!7 & sel) red
Drag select of 137 residues
> select up
1687 atoms, 1709 bonds, 226 residues, 1 model selected
> select up
3277 atoms, 3357 bonds, 429 residues, 1 model selected
> color sel orange
> select clear
> show #!8 models
> show #!13 models
> hide #!13 models
> show #!12 models
> volume #12 level 1.39
> select add #12
2 models selected
> view matrix models
> #12,0.48571,0.75293,-0.44405,97.149,-0.36186,0.63562,0.68194,-50.875,0.7957,-0.17054,0.58118,-5.3488
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.48571,0.75293,-0.44405,-81.762,-0.36186,0.63562,0.68194,1.008,0.7957,-0.17054,0.58118,-25.456
> hide #!12 models
> select subtract #12
Nothing selected
> select add #13
2 models selected
> show #!13 models
> view matrix models
> #13,0.3904,0.482,0.78439,-223.13,0.33881,0.71699,-0.60921,114.17,-0.85604,0.50359,0.11661,225.52
> volume #13 level 1.469
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.65346,0.09534,0.75093,-186,0.11602,0.9677,-0.22383,20.088,-0.74802,0.23339,0.62129,149.82
> view matrix models
> #13,0.88612,-0.40747,0.22084,-7.0707,-0.10495,-0.64052,-0.76074,534.11,0.45143,0.65092,-0.61034,85.324
> view matrix models
> #13,0.72742,-0.62402,-0.28542,185.12,-0.61847,-0.7764,0.12122,473.65,-0.29724,0.088351,-0.95071,437.48
> view matrix models
> #13,0.53954,-0.8382,-0.079465,224.63,-0.84196,-0.53749,-0.047096,505.24,-0.0032355,0.092316,-0.99572,385.98
> view matrix models
> #13,0.62703,-0.76632,-0.13998,204.42,-0.76603,-0.6392,0.067919,486.13,-0.14152,0.064639,-0.98782,418.75
> view matrix models
> #13,0.88145,0.46504,0.082382,-164.81,-0.26402,0.62983,-0.73048,284.36,-0.39159,0.62213,0.67794,-20.681
> view matrix models
> #13,0.88329,0.34827,0.31386,-191.25,0.049695,0.59614,-0.80134,242.71,-0.46619,0.72341,0.50925,10.179
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.88329,0.34827,0.31386,-106.61,0.049695,0.59614,-0.80134,222.09,-0.46619,0.72341,0.50925,62.54
> view matrix models
> #13,0.88329,0.34827,0.31386,-109.94,0.049695,0.59614,-0.80134,225.85,-0.46619,0.72341,0.50925,62.945
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.91159,0.36755,0.18416,-91.158,0.089086,0.2607,-0.9613,326.09,-0.40133,0.89272,0.20491,80.4
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.91159,0.36755,0.18416,-83.932,0.089086,0.2607,-0.9613,327,-0.40133,0.89272,0.20491,77.579
> view matrix models
> #13,0.91159,0.36755,0.18416,-84.949,0.089086,0.2607,-0.9613,324.38,-0.40133,0.89272,0.20491,83.436
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.94374,-0.28303,-0.171,128.56,-0.069424,0.33602,-0.93929,335.83,0.32331,0.89832,0.29746,-87.788
> hide #!8 models
> show #!11 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> view matrix models
> #13,0.38876,0.90043,0.19519,-95.278,-0.21732,0.2955,-0.9303,373.13,-0.89534,0.31924,0.31056,286.38
> fitmap #13 inMap #8
Fit map cryosparc_P141_J26_002_volume_map_sharp.mrc z flip in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 42381 points
correlation = 0.7094, correlation about mean = 0.3006, overlap = 1.028e+04
steps = 372, shift = 25.6, angle = 83.5 degrees
Position of cryosparc_P141_J26_002_volume_map_sharp.mrc z flip (#13) relative
to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.96410970 0.08725491 -0.25075700 37.64089028
-0.14247136 -0.62694205 -0.76592793 515.19639114
-0.22404107 0.77416423 -0.59200958 222.90910283
Axis 0.98891178 -0.01715462 -0.14751001
Axis point 0.00000000 204.15894680 238.87951769
Rotation angle (degrees) 128.86010122
Shift along axis -4.49580151
> undo
> show #!5 models
> hide #!5 models
> view matrix models
> #13,0.94727,-0.023846,-0.31954,104.55,-0.27009,0.47716,-0.83629,323.69,0.17241,0.87849,0.44556,-85.252
> show #!14 models
> view matrix models
> #13,0.77584,-0.41115,-0.47858,259.32,-0.41688,0.23531,-0.87798,415.74,0.47359,0.88067,0.011164,-51.364
> view matrix models
> #13,0.77801,-0.41578,-0.47098,258.19,-0.3914,0.26563,-0.88105,404.58,0.49143,0.86981,0.04392,-59.959
> select subtract #13
Nothing selected
> hide #!13 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!13 models
> select add #13
2 models selected
> view matrix models
> #13,0.75183,-0.46605,-0.46641,273.49,-0.24747,0.45621,-0.85477,327.68,0.61115,0.75807,0.22766,-101.19
> view matrix models
> #13,0.94999,-0.16376,-0.2659,122.45,-0.20483,0.31595,-0.9264,365.25,0.23572,0.93453,0.26661,-70.734
> view matrix models
> #13,0.96805,-0.21197,-0.13395,99.892,-0.10011,0.16304,-0.98153,389.1,0.2299,0.96358,0.13661,-46.967
> vop resample #13 onGrid #11
Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled as #15,
grid size 208,208,208, pixel 2, shown at step 1, values float32
> close #15
> hide #!14 models
> select subtract #13
Nothing selected
> show #!8 models
> volume #11 level 0.08821
> volume #11 level 0.1004
> vop resample #13 onGrid #11
Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled as #15,
grid size 208,208,208, pixel 2, shown at step 1, values float32
> hide #!8 models
> volume #12 level 1.598
> volume #15 level 1.696
> close #12
> close #13
> volume #15 level 1.487
> ui tool show "Segment Map"
Segmenting cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled,
density threshold 1.486514
Showing 8 region surfaces
213 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J26_002_volume_map_sharp z flip resampled.seg - 8
regions, 8 surfaces
Ungrouped to 2 regions
Ungrouped to 25 regions
> select #12.21
1 model selected
Ungrouped to 18 regions
> select #12.43
1 model selected
Ungrouped to 0 regions
> select #12.26
1 model selected
> select add #12.25
2 models selected
> select add #12.32
3 models selected
> select add #12.31
4 models selected
> select add #12.30
5 models selected
> select add #12.9
6 models selected
> select add #12.29
7 models selected
> select subtract #12.31
6 models selected
> select add #12.31
7 models selected
Grouped 7 regions
> select #12.34
1 model selected
> select add #12.20
2 models selected
> select add #12.33
3 models selected
> select add #12.18
4 models selected
> select add #12.19
5 models selected
Grouped 5 regions
> select #12.22
1 model selected
> select add #12.1
2 models selected
> hide #!11 models
> hide #!15 models
> show #!15 models
> hide #!7 models
> select #12.22
1 model selected
> select #12.2
1 model selected
> select add #12.41
2 models selected
> select add #12.22
3 models selected
> select add #12.16
4 models selected
> select add #12.17
5 models selected
> select subtract #12.16
4 models selected
> select add #12.15
5 models selected
> select add #12.23
6 models selected
> select add #12.24
7 models selected
Grouped 7 regions
> select add #12.16
2 models selected
> select add #12.10
3 models selected
> select add #12.4
4 models selected
> select add #12.6
5 models selected
> select add #12.7
6 models selected
> select add #12.1
7 models selected
> select subtract #12.7
6 models selected
Grouped 6 regions
> select add #12.43
2 models selected
> select add #12.37
3 models selected
> select subtract #12.37
2 models selected
> select add #12.7
3 models selected
Grouped 3 regions
> select add #12.39
2 models selected
> select add #12.37
3 models selected
Grouped 3 regions
> select add #12.40
2 models selected
> select add #12.36
3 models selected
Grouped 3 regions
> select #12.3
1 model selected
> select add #12.8
2 models selected
> select add #12.1
3 models selected
Grouped 3 regions
> select add #12.42
2 models selected
> select add #12.44
3 models selected
> select add #12.35
4 models selected
Grouped 4 regions
> view matrix models
> #12.1,0.46306,0.74641,-0.47795,121.51,-0.27886,0.63456,0.72081,-42.248,0.84131,-0.2005,0.50198,-54.824
> undo
> select clear
> select #12.27
1 model selected
> select add #12.28
2 models selected
Drag select of 233, 193 of 6492 triangles, 226, 673 of 5104 triangles, 215,
1541 of 7516 triangles, 248, 1005 of 17444 triangles, 15
cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled
> select #12.12
1 model selected
> select add #12.5
2 models selected
> select add #12.11
3 models selected
> select add #12.14
4 models selected
> select add #12.13
5 models selected
> select add #12.28
6 models selected
> select add #12.27
7 models selected
Grouped 7 regions
> hide #12.1 models
> show #12.1 models
> hide #!15 models
> hide #12.1 models
> show #12.1 models
> select clear
Drag select of 80, 240 of 360 triangles, 256, 10893 of 17716 triangles
Grouped 2 regions
> hide #12.1 models
> show #12.1 models
> hide #12.2 models
> show #12.2 models
> hide #12.9 models
> show #12.9 models
> hide #12.18 models
> hide #12.9 models
> hide #12.1 models
> color #12.2 darkgrey
> show #!15 models
> hide #!15 models
> show #!11 models
> select subtract #12.1
Nothing selected
> select add #12
5 models selected
> color #11 #945200ff models
> color #11 #941100ff models
> undo
> color #11 #d6d6d6ff models
> color #11 silver models
> color #12.2 #ff9300ff
> color #12.2 #8671ffff
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-57.407,0,1,0,-24.9,0,0,1,35.728
> volume #15 level 1.469
> hide #12.2 models
> show #12.2 models
> undo
> show #12.2 models
> undo
[Repeated 2 time(s)]
> show #12.1 models
> show #12.9 models
> show #12.18 models
> show #!14 models
> show #!10 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #12.9 models
> show #12.9 models
> hide #12.9 models
> show #12.9 models
> hide #12.9 models
> show #12.9 models
> hide #!5 models
> color #12.9 #ffd479ff
> color #12.9 #fffc79ff
> select #12.18
1 model selected
> color #12.9 #8671ffff
> color #12.9 #c1607eff
> color #12.9 #f2ad93ff
> color #12.9 #cd9f9bff
> color #12.9 #00f900ff
> color #12.9 #009051ff
> color #12.9 #008f00ff
> color #12.9 #009051ff
> color #12.9 #409191ff
> color #12.9 #5eaf88ff
> color #12.9 #a6ca8cff
> color #12.9 #8b9e70ff
> color #12.9 #9ea946ff
> color #12.9 #f8dd71ff
> color #12.9 #7974d0ff
> color #12.9 #e97d4dff
> color #12.9 #8ec9a4ff
> color #12.9 #3f8e97ff
> color #12.9 #008f00ff
> select clear
> fitmap #14 inMap #8
Fit molecule 4zyp_Mota_AM14.pdb (#14) to map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 16960 atoms
average map value = 0.1544, steps = 144
shifted from previous position = 0.528
rotated from previous position = 0.283 degrees
atoms outside contour = 7361, contour level = 0.15
Position of 4zyp_Mota_AM14.pdb (#14) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
-0.18010596 -0.98182955 0.05977107 201.36259741
-0.68922031 0.08260889 -0.71982716 242.93107209
0.70180995 -0.17084060 -0.69157522 205.54116766
Axis 0.61408494 -0.71817134 0.32730661
Axis point 171.66462494 0.00000000 189.54450963
Rotation angle (degrees) 153.44891129
Shift along axis 16.46258878
> show #!8 models
> hide #!12 models
> hide #!14 models
> show #!14 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
Segmenting cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled,
density threshold 1.468559
Showing 8 region surfaces
213 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J26_002_volume_map_sharp z flip resampled.seg - 8
regions, 8 surfaces
> hide #!12 models
> show #!12 models
> close #12
> volume #8 level 0.1022
> volume #8 level 0.108
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!8 models
> show #!10 models
> show #!5 models
> hide #!5 models
> show #!15 models
> hide #!15 models
Segmenting cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled,
density threshold 1.468559
Showing 8 region surfaces
213 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J26_002_volume_map_sharp z flip resampled.seg - 8
regions, 8 surfaces
Closing all segmentations.
> volume #10 level 0.09286
> fitmap #15 inMap #8
Fit map cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled in map
preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc using 42051 points
correlation = 0.7109, correlation about mean = 0.3055, overlap = 1.021e+04
steps = 312, shift = 33.6, angle = 52.2 degrees
Position of cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled (#15)
relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.94840554 0.16123937 0.27299962 -107.90053249
0.10051708 0.66371404 -0.74120172 211.54231643
-0.30070458 0.73040094 0.61326276 -2.34692398
Axis 0.93101412 0.36295580 -0.03841615
Axis point 0.00000000 130.36856314 237.80566180
Rotation angle (degrees) 52.21565226
Shift along axis -23.58624890
> undo
[Repeated 1 time(s)]
> show #!15 models
> undo
[Repeated 7 time(s)]
> show #!15 models
> select add #15
2 models selected
> view matrix models
> #15,0.94841,0.16124,0.273,-117.07,0.10052,0.66371,-0.7412,115.39,-0.3007,0.7304,0.61326,-43.209
> show #!11 models
> hide #!8 models
> view matrix models
> #15,0.94841,0.16124,0.273,-117.21,0.10052,0.66371,-0.7412,114.64,-0.3007,0.7304,0.61326,-43.651
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.95075,-0.061444,0.30381,-85.526,0.054946,0.99804,0.0299,-121.28,-0.30506,-0.011734,0.95226,7.4806
> show #!10 models
> view matrix models
> #15,0.95082,-0.063522,0.30317,-85.015,0.055902,0.99787,0.033756,-122.4,-0.30467,-0.015148,0.95234,7.9806
> view matrix models
> #15,0.92703,-0.16943,0.33453,-68.221,0.16804,0.98522,0.03331,-146.05,-0.33522,0.025336,0.9418,10.406
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.92703,-0.16943,0.33453,-39.098,0.16804,0.98522,0.03331,-48.065,-0.33522,0.025336,0.9418,85.943
> view matrix models
> #15,0.92703,-0.16943,0.33453,-33.43,0.16804,0.98522,0.03331,-40.38,-0.33522,0.025336,0.9418,80.326
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.89395,-0.39322,0.215,43.102,0.37568,0.91909,0.11893,-97.498,-0.24437,-0.025547,0.96935,61.648
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.89395,-0.39322,0.215,42.194,0.37568,0.91909,0.11893,-95.573,-0.24437,-0.025547,0.96935,68.382
> view matrix models
> #15,0.89395,-0.39322,0.215,32.807,0.37568,0.91909,0.11893,-106.51,-0.24437,-0.025547,0.96935,69.1
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.95561,-0.18569,0.22875,-21.817,0.18447,0.98247,0.026898,-51.155,-0.22973,0.016495,0.97311,57.299
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.95561,-0.18569,0.22875,-7.2447,0.18447,0.98247,0.026898,-42.602,-0.22973,0.016495,0.97311,61.164
> view matrix models
> #15,0.95561,-0.18569,0.22875,-11.006,0.18447,0.98247,0.026898,-43.599,-0.22973,0.016495,0.97311,62.893
> view matrix models
> #15,0.95561,-0.18569,0.22875,-14.643,0.18447,0.98247,0.026898,-44.671,-0.22973,0.016495,0.97311,66.237
> view matrix models
> #15,0.95561,-0.18569,0.22875,-25.201,0.18447,0.98247,0.026898,-48.132,-0.22973,0.016495,0.97311,67.734
> view matrix models
> #15,0.95561,-0.18569,0.22875,-15.536,0.18447,0.98247,0.026898,-48.418,-0.22973,0.016495,0.97311,60.254
> view matrix models
> #15,0.95561,-0.18569,0.22875,-13.424,0.18447,0.98247,0.026898,-46.58,-0.22973,0.016495,0.97311,58.127
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.97217,-0.09067,0.21604,-31.121,0.055836,0.98518,0.16221,-50.024,-0.22754,-0.14563,0.96282,89.014
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.97217,-0.09067,0.21604,-34.718,0.055836,0.98518,0.16221,-50.066,-0.22754,-0.14563,0.96282,91.458
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.98619,-0.084722,0.1423,-21.158,0.081732,0.9963,0.026738,-25.221,-0.14403,-0.014739,0.98946,42.301
> view matrix models
> #15,0.96344,-0.15336,0.21968,-22.402,0.20645,0.94757,-0.24391,20.138,-0.17075,0.28035,0.94459,6.7746
> view matrix models
> #15,0.93922,0.0051213,-0.34328,91.407,-0.031005,0.99707,-0.069955,24.223,0.34191,0.076347,0.93663,-73.828
> view matrix models
> #15,0.98223,0.010431,-0.18738,42.701,-0.014758,0.99966,-0.021709,8.3002,0.18708,0.024089,0.98205,-39.615
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.98223,0.010431,-0.18738,42.474,-0.014758,0.99966,-0.021709,12.727,0.18708,0.024089,0.98205,-37.476
> hide #!14 models
> show #!14 models
> select clear
> 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 #12
---
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 #!15 models
> hide #!11 models
> hide #!10 models
> color #14 #ff2600ff
> select clear
> show #!15 models
> hide #!12 models
> show #!12 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> ui mousemode right zoom
> hide #!12 atoms
> show #!12 cartoons
> hide #!15 models
> show #!14 models
Drag select of 1904 residues, 4 pseudobonds
> select up
15527 atoms, 15817 bonds, 4 pseudobonds, 2013 residues, 2 models selected
> select up
16960 atoms, 17299 bonds, 4 pseudobonds, 2200 residues, 2 models selected
> select #12/A:343
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 1454 residues, 3 pseudobonds
> select up
12478 atoms, 12694 bonds, 3 pseudobonds, 1610 residues, 3 models selected
> select up
20449 atoms, 20840 bonds, 3 pseudobonds, 2646 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!12 & sel to #14 & 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 4zyp_Mota_AM14.pdb, chain A (#14) with 4zyp_Mota_AM14.pdb, chain A
(#12), sequence alignment score = 2489.2
RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
0.000)
> show #!15 models
> select clear
> hide #!15 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
Drag select of 155 residues, 1 pseudobonds
Drag select of 144 residues
Drag select of 112 residues
Drag select of 246 residues, 1 pseudobonds
> select up
6977 atoms, 7116 bonds, 2 pseudobonds, 920 residues, 2 models selected
> select up
13030 atoms, 13358 bonds, 2 pseudobonds, 1706 residues, 2 models selected
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> color #12 #0433ffff
> color #12 #7a81ffff
> select clear
> hide #!14 models
> hide #!12 models
> show #!14 models
> show #!15 models
> color #14 #c1607eff
> select clear
> show #!12 models
> hide #!14 models
Drag select of 80 residues
> select up
1091 atoms, 1107 bonds, 144 residues, 1 model selected
> select up
3277 atoms, 3357 bonds, 429 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!15 models
> select #12/C:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/A:173
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
141 atoms, 140 bonds, 19 residues, 1 model selected
> select up
6964 atoms, 7081 bonds, 898 residues, 1 model selected
> select clear
> select add #12/C:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/A:218
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
252 atoms, 253 bonds, 30 residues, 1 model selected
> select up
6964 atoms, 7081 bonds, 898 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> show #!10 models
> hide #!10 models
> show #!7 models
> select #7/F:46
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12/B:224
15 atoms, 13 bonds, 2 residues, 2 models selected
> select up
292 atoms, 293 bonds, 36 residues, 2 models selected
> select up
6964 atoms, 7080 bonds, 898 residues, 2 models selected
> select up
6965 atoms, 7080 bonds, 899 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!7 & sel to #12 & 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 4zyp_Mota_AM14.pdb, chain B (#12) with 5udc.pdb, chain F (#7),
sequence alignment score = 2356
RMSD between 433 pruned atom pairs is 0.628 angstroms; (across all 448 pairs:
0.827)
> select clear
> show #!15 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!15 models
> select add #15
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.88629,0.30254,0.35066,-117.74,-0.38278,0.90474,0.18687,64.443,-0.26072,-0.29984,0.91767,139.72
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.88629,0.30254,0.35066,-131.83,-0.38278,0.90474,0.18687,61.754,-0.26072,-0.29984,0.91767,147.47
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.7604,0.46961,0.44861,-156.15,-0.62785,0.70823,0.32283,120.67,-0.16612,-0.52714,0.83338,186.47
> view matrix models
> #15,0.85017,0.31753,0.41999,-142.92,-0.4089,0.9007,0.14675,78.257,-0.33169,-0.29649,0.89559,168.68
> view matrix models
> #15,0.86333,0.34985,0.36368,-138.09,-0.39526,0.91684,0.056318,94.133,-0.31374,-0.19237,0.92982,137.66
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.86333,0.34985,0.36368,-139.16,-0.39526,0.91684,0.056318,91.132,-0.31374,-0.19237,0.92982,142.75
> view matrix models
> #15,0.86333,0.34985,0.36368,-139.82,-0.39526,0.91684,0.056318,91.396,-0.31374,-0.19237,0.92982,141.6
> hide #!15 models
> show #!15 models
> volume flip #15
Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled z flip as
#13, grid size 208,208,208, pixel 2, shown at step 1, values float32
> hide #!12 models
> show #!12 models
> hide #!7 models
> show #!7 models
> hide #!13 models
> hide #!12 models
Drag select of 591 residues, 1 pseudobonds
> select up
4996 atoms, 5086 bonds, 1 pseudobond, 647 residues, 4 models selected
> select up
6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 4 models selected
> show #!12 models
Drag select of 185 residues
> select up
8797 atoms, 8974 bonds, 1 pseudobond, 1146 residues, 5 models selected
> select up
9956 atoms, 10174 bonds, 1 pseudobond, 1301 residues, 5 models selected
> combine #7,12
Remapping chain ID 'L' in 4zyp_Mota_AM14.pdb #12 to 'M'
> hide #!12 models
> select add #12
13438 atoms, 13714 bonds, 3 pseudobonds, 1750 residues, 6 models selected
> select subtract #12
6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 4 models selected
> hide #!7 models
> select add #7
6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 4 models selected
> select subtract #7
2 models selected
> select #16/B:52
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
82 atoms, 84 bonds, 10 residues, 1 model selected
> select up
3482 atoms, 3540 bonds, 449 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "/Users/szhang3/OneDrive - Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb"
> models #16 relModel #11
> ui mousemode right zoom
> show #!15 models
> show #!13 models
> hide #!15 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #13
2 models selected
> view matrix models
> #13,-0.58926,0.23529,-0.77293,412.56,0.60259,0.76525,-0.22644,-64.47,0.53821,-0.59918,-0.59272,277.85
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.58926,0.23529,-0.77293,450.96,0.60259,0.76525,-0.22644,-70.226,0.53821,-0.59918,-0.59272,329.99
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.69746,-0.20934,-0.68536,540.28,0.2257,0.84353,-0.48735,48.007,0.68015,-0.4946,-0.54108,269.57
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.69746,-0.20934,-0.68536,509.91,0.2257,0.84353,-0.48735,57.162,0.68015,-0.4946,-0.54108,275.59
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.71657,0.34654,-0.60534,401.53,0.54335,0.82151,-0.1729,-66.549,0.43737,-0.45281,-0.77696,364.93
> open /Users/szhang3/Downloads/cryosparc_P141_J33_003_volume_map_sharp.mrc
Opened cryosparc_P141_J33_003_volume_map_sharp.mrc as #17, grid size
208,208,208, pixel 2, shown at level 0.146, step 1, values float32
> volume #17 level 1.218
> hide #!13 models
> select subtract #13
Nothing selected
> volume #17 level 1.153
> volume #17 level 1.244
> open /Users/szhang3/Downloads/cryosparc_P141_J33_003_volume_map.mrc
Opened cryosparc_P141_J33_003_volume_map.mrc as #18, grid size 208,208,208,
pixel 2, shown at level 0.0925, step 1, values float32
> volume #18 level 1.008
> volume #18 level 1.352
> volume #18 level 1.264
> select add #18
2 models selected
> view matrix models
> #18,-0.98508,0.15839,-0.067283,388.97,0.075864,0.75064,0.65634,-87.645,0.15446,0.64145,-0.75146,165.29
> view matrix models
> #18,-0.90282,0.38096,-0.19947,348.98,0.016118,0.4935,0.8696,-60.385,0.42972,0.78187,-0.45168,20.226
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.90282,0.38096,-0.19947,371.3,0.016118,0.4935,0.8696,-109.55,0.42972,0.78187,-0.45168,71.611
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.90158,0.35858,-0.24201,384.09,0.016012,0.5867,0.80964,-118.26,0.43232,0.72608,-0.5347,99.16
> view matrix models
> #18,-0.82464,0.49676,0.27056,239.61,0.47175,0.34004,0.81353,-159.62,0.31212,0.7985,-0.51476,104.44
> view matrix models
> #18,-0.85261,0.51254,0.10174,274.41,0.33842,0.39326,0.85488,-151.57,0.39815,0.76332,-0.50875,93.143
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.85261,0.51254,0.10174,248.3,0.33842,0.39326,0.85488,-142.61,0.39815,0.76332,-0.50875,120.5
> select up
40612 atoms, 41463 bonds, 5277 residues, 32 models selected
> select up
40612 atoms, 41463 bonds, 5277 residues, 32 models selected
> volume flip #18
Opened cryosparc_P141_J33_003_volume_map.mrc z flip as #19, grid size
208,208,208, pixel 2, shown at step 1, values float32
> view matrix models
> #1,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#2,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#3,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#4,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#5,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#6,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#8,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#9,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#10,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#11,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#7,-0.20511,0.82965,-0.51924,138.92,0.82206,-0.14189,-0.55144,177.56,-0.53118,-0.53995,-0.65292,196.49,#14,-0.18011,-0.98183,0.059771,201.28,-0.68922,0.082609,-0.71983,242.99,0.70181,-0.17084,-0.69158,205.43,#15,0.86333,0.34985,0.36368,-139.9,-0.39526,0.91684,0.056318,91.458,-0.31374,-0.19237,0.92982,141.49,#12,-0.18011,-0.98183,0.059771,201.28,-0.68922,0.082609,-0.71983,242.99,0.70181,-0.17084,-0.69158,205.43,#13,-0.71657,0.34654,-0.60534,401.45,0.54335,0.82151,-0.1729,-66.488,0.43737,-0.45281,-0.77696,364.82,#16,-0.20511,0.82965,-0.51924,138.92,0.82206,-0.14189,-0.55144,177.56,-0.53118,-0.53995,-0.65292,196.49,#17,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#18,-0.85261,0.51254,0.10174,248.23,0.33842,0.39326,0.85488,-142.54,0.39815,0.76332,-0.50875,120.39
> view matrix models
> #1,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#2,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#3,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#4,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#5,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#6,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#8,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#9,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#10,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#11,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#7,-0.20511,0.82965,-0.51924,138.78,0.82206,-0.14189,-0.55144,176.87,-0.53118,-0.53995,-0.65292,196.63,#14,-0.18011,-0.98183,0.059771,201.15,-0.68922,0.082609,-0.71983,242.3,0.70181,-0.17084,-0.69158,205.58,#15,0.86333,0.34985,0.36368,-140.04,-0.39526,0.91684,0.056318,90.767,-0.31374,-0.19237,0.92982,141.63,#12,-0.18011,-0.98183,0.059771,201.15,-0.68922,0.082609,-0.71983,242.3,0.70181,-0.17084,-0.69158,205.58,#13,-0.71657,0.34654,-0.60534,401.31,0.54335,0.82151,-0.1729,-67.178,0.43737,-0.45281,-0.77696,364.96,#16,-0.20511,0.82965,-0.51924,138.78,0.82206,-0.14189,-0.55144,176.87,-0.53118,-0.53995,-0.65292,196.63,#17,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#18,-0.85261,0.51254,0.10174,248.09,0.33842,0.39326,0.85488,-143.23,0.39815,0.76332,-0.50875,120.54
> select subtract #18
40612 atoms, 41463 bonds, 5277 residues, 30 models selected
> select subtract #17
40612 atoms, 41463 bonds, 5277 residues, 28 models selected
> select subtract #15
40612 atoms, 41463 bonds, 5277 residues, 26 models selected
> select add #14
40612 atoms, 41463 bonds, 5 pseudobonds, 5277 residues, 27 models selected
> select subtract #13
40612 atoms, 41463 bonds, 5 pseudobonds, 5277 residues, 25 models selected
> select subtract #14
23652 atoms, 24164 bonds, 3077 residues, 23 models selected
> select add #13
23652 atoms, 24164 bonds, 3077 residues, 25 models selected
> select add #12
23652 atoms, 24164 bonds, 2 pseudobonds, 3077 residues, 26 models selected
> select subtract #11
23652 atoms, 24164 bonds, 2 pseudobonds, 3077 residues, 24 models selected
> select subtract #12
16933 atoms, 17303 bonds, 2204 residues, 22 models selected
> select subtract #13
16933 atoms, 17303 bonds, 2204 residues, 20 models selected
> select add #16
16933 atoms, 17303 bonds, 3 pseudobonds, 2204 residues, 22 models selected
> select subtract #16
6848 atoms, 6991 bonds, 890 residues, 19 models selected
> select subtract #1
6848 atoms, 6991 bonds, 890 residues, 17 models selected
> select subtract #2
6848 atoms, 6991 bonds, 890 residues, 15 models selected
> select subtract #4
6848 atoms, 6991 bonds, 890 residues, 13 models selected
> select subtract #3
6848 atoms, 6991 bonds, 890 residues, 11 models selected
> select subtract #5
6848 atoms, 6991 bonds, 890 residues, 9 models selected
> select subtract #6
6848 atoms, 6991 bonds, 890 residues, 7 models selected
> select subtract #8
6848 atoms, 6991 bonds, 890 residues, 5 models selected
> select add #7
6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 6 models selected
> select subtract #9
6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 4 models selected
> select subtract #7
2 models selected
> select subtract #10
Nothing selected
> select add #19
2 models selected
> view matrix models
> #19,-0.85261,0.51254,0.10174,236.5,0.33842,0.39326,0.85488,-144.07,0.39815,0.76332,-0.50875,98.202
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.91805,0.052648,0.39295,285.43,-0.31286,-0.70499,-0.63648,560.09,0.24351,-0.70726,0.66369,189.86
> view matrix models
> #19,0.89378,0.43488,-0.10971,-60.834,-0.34247,0.5038,-0.79303,338.15,-0.2896,0.74637,0.59922,-1.6195
> view matrix models
> #19,0.92863,0.10557,-0.35568,58.1,-0.33168,0.66578,-0.66837,273.06,0.16625,0.73864,0.65327,-106.19
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.92863,0.10557,-0.35568,69.057,-0.33168,0.66578,-0.66837,246.3,0.16625,0.73864,0.65327,-95.497
> view matrix models
> #19,0.92863,0.10557,-0.35568,68.853,-0.33168,0.66578,-0.66837,237.97,0.16625,0.73864,0.65327,-96.946
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.9149,-0.22501,-0.33517,139.01,-0.20446,0.45762,-0.86532,300.59,0.34808,0.86021,0.37267,-98.742
> view matrix models
> #19,0.81984,0.27041,-0.50471,88.562,-0.57248,0.40365,-0.71367,354.79,0.010746,0.87404,0.48574,-57.071
> view matrix models
> #19,0.83637,0.35676,-0.41619,46.74,-0.53801,0.67975,-0.49849,239.92,0.10506,0.64083,0.76046,-86.8
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.83637,0.35676,-0.41619,60.477,-0.53801,0.67975,-0.49849,259.66,0.10506,0.64083,0.76046,-80.504
> view matrix models
> #19,0.83637,0.35676,-0.41619,80.111,-0.53801,0.67975,-0.49849,253.2,0.10506,0.64083,0.76046,-77.294
> view matrix models
> #19,0.83637,0.35676,-0.41619,78.412,-0.53801,0.67975,-0.49849,252.55,0.10506,0.64083,0.76046,-81.818
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.70058,-0.15608,-0.69629,280.1,-0.26867,0.84628,-0.46004,152.13,0.66106,0.50937,0.55095,-121.74
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.70058,-0.15608,-0.69629,234.18,-0.26867,0.84628,-0.46004,164.89,0.66106,0.50937,0.55095,-118.4
> view matrix models
> #19,0.70058,-0.15608,-0.69629,236.24,-0.26867,0.84628,-0.46004,169.88,0.66106,0.50937,0.55095,-122.69
> view matrix models
> #19,0.70058,-0.15608,-0.69629,235.87,-0.26867,0.84628,-0.46004,169.88,0.66106,0.50937,0.55095,-118.48
> view matrix models
> #19,0.70058,-0.15608,-0.69629,234.52,-0.26867,0.84628,-0.46004,171.08,0.66106,0.50937,0.55095,-119.1
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.61078,-0.38767,-0.6904,302.13,-0.079273,0.83762,-0.54047,151.64,0.78782,0.38484,0.48087,-102.7
> open /Users/szhang3/Downloads/6oe5.cif
6oe5.cif title:
Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs [more
info...]
Chain information for 6oe5.cif #20
---
Chain | Description | UniProt
A | Fusion glycoprotein F0,Fibritin | FUS_HRSVA 1-513, WAC_BPT4 518-544
B | Motavizumab Fab Heavy Chain |
C | Motavizumab Fab Light Chain |
H | CR9501 Fab Heavy Chain |
L | CR9501 Fab Light Chain |
> hide #!16,20 atoms
> show #!16,20 cartoons
> select add #20
8527 atoms, 8716 bonds, 8 pseudobonds, 1113 residues, 4 models selected
> select subtract #19
8527 atoms, 8716 bonds, 8 pseudobonds, 1113 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #20,1,0,0,63.799,0,1,0,9.3042,0,0,1,25.952
> view matrix models #20,1,0,0,97.251,0,1,0,69.114,0,0,1,172.29
> view matrix models #20,1,0,0,94.477,0,1,0,77.895,0,0,1,190.66
> view matrix models #20,1,0,0,84.039,0,1,0,100.28,0,0,1,213.23
> hide #!19 models
> select clear
> select add #20/A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #16/F:303
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
191 atoms, 194 bonds, 24 residues, 2 models selected
> select up
3692 atoms, 3753 bonds, 475 residues, 2 models selected
> select up
3706 atoms, 3766 bonds, 477 residues, 2 models selected
> select up
3910 atoms, 3971 bonds, 502 residues, 2 models selected
> select up
3921 atoms, 3981 bonds, 504 residues, 2 models selected
> select up
4372 atoms, 4435 bonds, 565 residues, 2 models selected
> select up
5458 atoms, 5535 bonds, 702 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!20 & sel to #16 & 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 combination, chain F (#16) with 6oe5.cif, chain A (#20), sequence
alignment score = 2210
RMSD between 231 pruned atom pairs is 0.920 angstroms; (across all 250 pairs:
1.163)
> hide #!20 models
> show #!20 models
> show #!19 models
> select add #20
12010 atoms, 12256 bonds, 8 pseudobonds, 1563 residues, 3 models selected
> select subtract #20
3483 atoms, 3540 bonds, 450 residues, 1 model selected
> select add #16
10085 atoms, 10312 bonds, 3 pseudobonds, 1314 residues, 3 models selected
> select subtract #16
Nothing selected
> select add #19
2 models selected
> view matrix models
> #19,0.61078,-0.38767,-0.6904,308.55,-0.079273,0.83762,-0.54047,151.76,0.78782,0.38484,0.48087,-97.761
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,538.89,0.10987,0.30807,-0.945,317.49,0.58882,-0.78614,-0.18782,346.25
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,509.71,0.10987,0.30807,-0.945,315.5,0.58882,-0.78614,-0.18782,324.22
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,508.19,0.10987,0.30807,-0.945,315.78,0.58882,-0.78614,-0.18782,322.46
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,512.36,0.10987,0.30807,-0.945,317.67,0.58882,-0.78614,-0.18782,324.84
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,516.86,0.10987,0.30807,-0.945,315.66,0.58882,-0.78614,-0.18782,321.47
> select subtract #19
Nothing selected
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!20 models
> show #!20 models
> show #!18 models
> ui mousemode right "rotate selected models"
> select add #18
2 models selected
> view matrix models
> #18,-0.97509,0.11284,0.19099,343.15,0.2208,0.5765,0.7867,-145.64,-0.021337,0.80927,-0.58705,212.34
> view matrix models
> #18,0.57224,-0.33586,0.74816,13.639,-0.62888,0.40582,0.66319,90.899,-0.52635,-0.85001,0.021009,560.59
> view matrix models
> #18,0.16891,-0.57784,0.79848,139.97,-0.5889,0.59045,0.55187,63.893,-0.79036,-0.56344,-0.24056,603.17
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.16891,-0.57784,0.79848,114.93,-0.5889,0.59045,0.55187,89.792,-0.79036,-0.56344,-0.24056,571.87
> view matrix models
> #18,0.16891,-0.57784,0.79848,114.64,-0.5889,0.59045,0.55187,74.173,-0.79036,-0.56344,-0.24056,574.35
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.16911,-0.54739,0.81962,103.91,-0.56567,0.62708,0.53552,64.549,-0.8071,-0.5542,-0.20359,568.7
> view matrix models
> #18,0.55936,-0.49561,0.66445,41.794,-0.51538,0.41988,0.74705,58.531,-0.64924,-0.76031,-0.020565,545.68
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.55936,-0.49561,0.66445,58.699,-0.51538,0.41988,0.74705,54.872,-0.64924,-0.76031,-0.020565,530.41
> view matrix models
> #18,0.55936,-0.49561,0.66445,51.512,-0.51538,0.41988,0.74705,55.959,-0.64924,-0.76031,-0.020565,521.99
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.13793,-0.70247,0.69822,177.13,-0.43583,0.58999,0.67968,15.48,-0.8894,-0.39805,-0.22478,532.15
> view matrix models
> #18,0.1326,-0.7026,0.69913,178.09,-0.43325,0.59332,0.67843,14.463,-0.89147,-0.39285,-0.22572,531.63
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.1326,-0.7026,0.69913,176.88,-0.43325,0.59332,0.67843,17.209,-0.89147,-0.39285,-0.22572,537.57
> hide #!18 models
> select subtract #18
Nothing selected
> show #!19 models
> transparency #18,20 50
> transparency #18,19 50
> hide #!19 models
> hide #!20 models
> show #!20 models
Drag select of 286 residues, 1 pseudobonds
> select up
2678 atoms, 2744 bonds, 1 pseudobond, 354 residues, 2 models selected
> select up
3237 atoms, 3321 bonds, 1 pseudobond, 424 residues, 2 models selected
> color (#!20 & sel) yellow
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
Drag select of 244 residues
> select up
6025 atoms, 6163 bonds, 1 pseudobond, 791 residues, 3 models selected
> select up
8148 atoms, 8362 bonds, 1 pseudobond, 1073 residues, 3 models selected
> select up
18612 atoms, 19028 bonds, 8 pseudobonds, 2427 residues, 3 models selected
> select down
8148 atoms, 8362 bonds, 1 pseudobond, 1073 residues, 3 models selected
> select add #20/L:185
8156 atoms, 8369 bonds, 1 pseudobond, 1074 residues, 3 models selected
> select up
8191 atoms, 8405 bonds, 1 pseudobond, 1078 residues, 3 models selected
> select up
9789 atoms, 10042 bonds, 1 pseudobond, 1285 residues, 3 models selected
> delete atoms (#!16,20 & sel)
> delete bonds (#!16,20 & sel)
> undo
Undo failed, probably because structures have been modified.
> hide #!20 models
> show #!20 models
> close #20
> open /Users/szhang3/Downloads/6oe5.cif
6oe5.cif title:
Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs [more
info...]
Chain information for 6oe5.cif #20
---
Chain | Description | UniProt
A | Fusion glycoprotein F0,Fibritin | FUS_HRSVA 1-513, WAC_BPT4 518-544
B | Motavizumab Fab Heavy Chain |
C | Motavizumab Fab Light Chain |
H | CR9501 Fab Heavy Chain |
L | CR9501 Fab Light Chain |
> select #20/A:88@ND2
1 atom, 1 residue, 1 model selected
> select add #16/F:169
7 atoms, 5 bonds, 2 residues, 2 models selected
> select up
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
264 atoms, 263 bonds, 33 residues, 2 models selected
> select up
3700 atoms, 3758 bonds, 476 residues, 2 models selected
> select up
3782 atoms, 3838 bonds, 487 residues, 2 models selected
> select up
4372 atoms, 4435 bonds, 565 residues, 2 models selected
> select up
5458 atoms, 5535 bonds, 702 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!20 & sel to #16 & 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 combination, chain F (#16) with 6oe5.cif, chain A (#20), sequence
alignment score = 2210
RMSD between 231 pruned atom pairs is 0.920 angstroms; (across all 250 pairs:
1.163)
> matchmaker #!20 & sel to #16 & 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 combination, chain F (#16) with 6oe5.cif, chain A (#20), sequence
alignment score = 2210
RMSD between 231 pruned atom pairs is 0.920 angstroms; (across all 250 pairs:
1.163)
> select clear
> select #20/L:5@CB
1 atom, 1 residue, 1 model selected
> select add #20/H:85@CB
2 atoms, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
53 atoms, 51 bonds, 8 residues, 1 model selected
> select up
3315 atoms, 3400 bonds, 437 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!16,20 atoms
> show #!16,20 cartoons
> hide #!20 models
> show #!20 models
> hide #!20 models
Drag select of 327 residues, 1 pseudobonds
> select up
2939 atoms, 2989 bonds, 1 pseudobond, 381 residues, 2 models selected
> select up
3482 atoms, 3540 bonds, 1 pseudobond, 449 residues, 2 models selected
> delete atoms (#!16 & sel)
> delete bonds (#!16 & sel)
> show #!20 models
> undo
[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.
> show #!14 models
> select clear
> select add #14/A:81
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 8 residues
Drag select of 17 residues
Drag select of 114 residues
Drag select of 80 residues
> select up
3258 atoms, 3300 bonds, 431 residues, 1 model selected
> select up
13478 atoms, 13759 bonds, 1751 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!14 models
> show #!14 models
> hide #!16 models
> show #!16 models
> show #!20 models
> hide #!16 models
> hide #!14 models
Drag select of 174 residues, 1 pseudobonds
Drag select of 46 residues, 4 pseudobonds
> select up
561 atoms, 571 bonds, 4 pseudobonds, 70 residues, 2 models selected
> select up
1295 atoms, 1313 bonds, 4 pseudobonds, 162 residues, 2 models selected
> select up
1309 atoms, 1326 bonds, 4 pseudobonds, 164 residues, 2 models selected
> select up
1513 atoms, 1531 bonds, 4 pseudobonds, 189 residues, 2 models selected
> select up
1524 atoms, 1541 bonds, 4 pseudobonds, 191 residues, 2 models selected
> select up
1975 atoms, 1995 bonds, 4 pseudobonds, 252 residues, 2 models selected
> select up
5212 atoms, 5316 bonds, 8 pseudobonds, 676 residues, 2 models selected
> select down
1975 atoms, 1995 bonds, 4 pseudobonds, 252 residues, 2 models selected
> delete atoms (#!20 & sel)
> delete bonds (#!20 & sel)
> show #!16 models
> show #!14 models
> combine #14,16,20
Remapping chain ID 'B' in 6oe5.cif #20 to 'D'
> hide #!20 models
> hide #!16 models
> hide #!14 models
> save "/Users/szhang3/OneDrive - Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb"
> models #21 relModel #11
Drag select of 283 residues, 1 pseudobonds
> select up
2523 atoms, 2571 bonds, 1 pseudobond, 326 residues, 2 models selected
> select up
3482 atoms, 3540 bonds, 1 pseudobond, 449 residues, 2 models selected
> color (#!21 & sel) gray
> select clear
Drag select of 157 residues, 1 pseudobonds
> select up
1661 atoms, 1689 bonds, 1 pseudobond, 225 residues, 2 models selected
> select up
3237 atoms, 3321 bonds, 1 pseudobond, 424 residues, 2 models selected
> color (#!21 & sel) yellow
> select clear
Drag select of 275 residues, 1 pseudobonds
> select up
2564 atoms, 2612 bonds, 1 pseudobond, 342 residues, 2 models selected
> select up
3237 atoms, 3313 bonds, 1 pseudobond, 428 residues, 2 models selected
> color (#!21 & sel) red
> select clear
> show #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!17 models
> close #17
> hide #!19 models
> hide #!18 models
> show #!19 models
> select add #19
2 models selected
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,518.3,0.10987,0.30807,-0.945,314.19,0.58882,-0.78614,-0.18782,317.2
> hide #!19 models
> select subtract #19
Nothing selected
> select add #18
2 models selected
> show #!18 models
> view matrix models
> #18,0.1326,-0.7026,0.69913,176.64,-0.43325,0.59332,0.67843,16.803,-0.89147,-0.39285,-0.22572,538.2
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.33468,-0.78412,0.52262,324.92,-0.40325,0.62044,0.67264,5.8168,-0.85169,0.014377,-0.52385,498.75
> view matrix models
> #18,-0.36878,-0.74911,0.55031,319.03,-0.46103,0.6615,0.5915,24.437,-0.80713,-0.035575,-0.58931,512.98
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.36878,-0.74911,0.55031,317.62,-0.46103,0.6615,0.5915,27.356,-0.80713,-0.035575,-0.58931,516.04
> view matrix models
> #18,-0.36878,-0.74911,0.55031,312.99,-0.46103,0.6615,0.5915,29.075,-0.80713,-0.035575,-0.58931,516.96
> view matrix models
> #18,-0.36878,-0.74911,0.55031,315.43,-0.46103,0.6615,0.5915,28.326,-0.80713,-0.035575,-0.58931,513.05
> view matrix models
> #18,-0.36878,-0.74911,0.55031,317.05,-0.46103,0.6615,0.5915,27.767,-0.80713,-0.035575,-0.58931,510.95
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.41005,-0.69265,0.59338,305.04,-0.52738,0.71086,0.46535,55.007,-0.74413,-0.12212,-0.65678,529.71
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.41005,-0.69265,0.59338,299.33,-0.52738,0.71086,0.46535,55.582,-0.74413,-0.12212,-0.65678,529.95
> show #!19 models
> select add #19
4 models selected
> select subtract #18
2 models selected
> hide #!18 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!12 models
> close #12
> 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 #12
---
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 |
> view matrix models
> #19,-0.80076,-0.53579,-0.26777,513.82,0.10987,0.30807,-0.945,301.58,0.58882,-0.78614,-0.18782,317.77
> undo
> hide #!12,21 atoms
> show #!12,21 cartoons
> ui mousemode right zoom
> hide #!19 models
> select subtract #19
Nothing selected
> select #21/B:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
204 atoms, 204 bonds, 25 residues, 1 model selected
> select up
3482 atoms, 3540 bonds, 449 residues, 1 model selected
> select add #12/A:493
3488 atoms, 3545 bonds, 450 residues, 2 models selected
> select up
3658 atoms, 3716 bonds, 471 residues, 2 models selected
> select up
6964 atoms, 7080 bonds, 898 residues, 2 models selected
> select up
40075 atoms, 40968 bonds, 5220 residues, 2 models selected
> select down
6964 atoms, 7080 bonds, 898 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!12 & sel to #21 & 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 combination, chain B (#21) with 4zyp_Mota_AM14.pdb, chain A (#12),
sequence alignment score = 2468.2
RMSD between 449 pruned atom pairs is 0.308 angstroms; (across all 449 pairs:
0.308)
> select clear
> hide #!21 models
> show #!21 models
> hide #!21 models
Drag select of 168 residues
Drag select of 156 residues
Drag select of 168 residues, 1 pseudobonds
Drag select of 141 residues, 1 pseudobonds
Drag select of 255 residues, 1 pseudobonds
Drag select of 130 residues
> select up
10139 atoms, 10311 bonds, 3 pseudobonds, 1356 residues, 2 models selected
> select up
19544 atoms, 20036 bonds, 3 pseudobonds, 2559 residues, 2 models selected
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> show #!21 models
> show #!18 models
> hide #!18 models
> show #!19 models
> fitmap #21 inMap #19
Fit molecule combination (#21) to map cryosparc_P141_J33_003_volume_map.mrc z
flip (#19) using 10085 atoms
average map value = 1.638, steps = 60
shifted from previous position = 1.21
rotated from previous position = 4.44 degrees
atoms outside contour = 1422, contour level = 1.264
Position of combination (#21) relative to
cryosparc_P141_J33_003_volume_map.mrc z flip (#19) coordinates:
Matrix rotation and translation
0.46228095 0.72823210 -0.50593906 179.40738253
-0.65307841 0.66556354 0.36126688 232.06673071
0.59982073 0.16341108 0.78327001 172.74635996
Axis -0.11112916 -0.62106927 -0.77583714
Axis point 126.78666523 -107.25329339 0.00000000
Rotation angle (degrees) 62.89920534
Shift along axis -298.08994989
> hide #!19 models
Drag select of 27 residues
> select up
544 atoms, 544 bonds, 68 residues, 2 models selected
> select up
10446 atoms, 10620 bonds, 1347 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!12 & sel to #21 & 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 combination, chain B (#21) with 4zyp_Mota_AM14.pdb, chain B (#12),
sequence alignment score = 2486.8
RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
0.000)
> select clear
> show #!19 models
> volume #19 level 1.817
> volume #19 level 1.701
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
> true
> rename #21 mono_MEDI_Mota
> show #!16 models
> hide #!16 models
> close #16
> close #15
> close #13
> show #!18 models
> hide #!18 models
> show #!11 models
> volume #19 level 1.162
> select add #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.32797,0.67647,-0.65941,292.11,0.1516,0.72666,0.67006,-130.35,0.93245,0.11979,-0.34088,86.988
> view matrix models
> #11,-0.39571,0.49844,-0.77134,369.49,0.056922,0.8516,0.5211,-101.99,0.91661,0.1623,-0.36536,87.116
> fitmap #11 inMap #8
Fit map RSV monomer.mrc in map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc using
10770 points
correlation = 0.9671, correlation about mean = 0.6097, overlap = 584.8
steps = 80, shift = 7.11, angle = 5.6 degrees
Position of RSV monomer.mrc (#11) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
-0.48067845 0.45566289 -0.74921263 384.77138142
0.04115820 0.86517263 0.49978228 -93.74623885
0.87593050 0.20939832 -0.43462410 100.84505324
Axis -0.17060091 -0.95477347 -0.24352198
Axis point 171.33930350 0.00000000 174.78961288
Rotation angle (degrees) 121.67261641
Shift along axis -0.69391379
> ui mousemode right zoom
> hide #!11 models
> select subtract #11
Nothing selected
Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip, density threshold
1.161735
Showing 8 region surfaces
30 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J33_003_volume_map z flip.seg - 8 regions, 8 surfaces
Closing all segmentations.
> show #!11 models
> hide #!11 models
> vop resample #18,19 onGrid #11
Opened cryosparc_P141_J33_003_volume_map.mrc resampled as #13, grid size
208,208,208, pixel 2, shown at step 1, values float32
Opened cryosparc_P141_J33_003_volume_map.mrc z flip resampled as #15, grid
size 208,208,208, pixel 2, shown at step 1, values float32
> close #18
> close #19
> hide #!13 models
Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip resampled, density
threshold 1.161735
Showing 8 region surfaces
24 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J33_003_volume_map z flip resampled.seg - 8 regions, 8
surfaces
Closing all segmentations.
> show #!8 models
> hide #!8 models
> show #!11 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip resampled, density
threshold 1.161735
Showing 8 region surfaces
24 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J33_003_volume_map z flip resampled.seg - 8 regions, 8
surfaces
Closing all segmentations.
> vop resample #113,15 onGrid #8
Opened cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled as
#16, grid size 208,208,208, pixel 2, shown at step 1, values float32
> close #13
> close #15
> hide #!16 models
> show #!16 models
> color #16 #5eaf88ff models
> color #16 #8ec9a4ff models
> transparency #16 50
> hide #!11 models
Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled,
density threshold 1.161735
Showing 8 region surfaces
25 watershed regions, grouped to 8 regions
Showing cryosparc_P141_J33_003_volume_map z flip resampled resampled.seg - 8
regions, 8 surfaces
> select #13.4
1 model selected
> select add #13.2
2 models selected
Grouped 2 regions
> select #13.8
1 model selected
> select add #13.1
2 models selected
> select #13.1
1 model selected
Ungrouped to 2 regions
> select #13.8
1 model selected
> select add #13.5
2 models selected
> select add #13.9
3 models selected
Grouped 3 regions
> select #13.6
1 model selected
> select add #13.4
2 models selected
Grouped 2 regions
> select #13.3
1 model selected
> select add #13.7
2 models selected
Grouped 2 regions
> select #13.3
1 model selected
> hide #13.1 models
> show #13.1 models
> color #13.1 #f8dd71ff
> color #13.1 #fbe9a8ff
> color #13.3 #ff7e79ff
> select clear
> select #13.4
1 model selected
> color #13.3 #d6d6d6ff
> color #13.3 #ff7e79ff
> select #13.4
1 model selected
> hide #13.3 models
> show #13.3 models
> hide #13.4 models
> show #13.4 models
> color #13.4 silver
> color #13.4 #d6d6d6ff
> select clear
> hide #13.4 models
> hide #!16 models
> hide #!12 models
> hide #!13 models
> hide #13.1 models
> hide #13.2 models
> hide #13.3 models
> show #!16 models
> hide #!16 models
> show #13.4 models
> hide #13.4 models
> show #13.3 models
> hide #13.3 models
> show #13.2 models
> hide #!21 models
> show #!21 models
> hide #13.2 models
> show #13.2 models
> hide #13.2 models
> show #13.2 models
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
> true
> show #!16 models
> hide #13.2 models
Cell requested for row 14 is out of bounds for table with 21 rows! Resizing
table model.
> open /Users/szhang3/Downloads/cryosparc_P141_J34_002_volume_map_sharp.mrc
Opened cryosparc_P141_J34_002_volume_map_sharp.mrc as #15, grid size
208,208,208, pixel 2, shown at level 0.135, step 1, values float32
> volume #15 level 0.8685
> volume #15 level 1.453
> open /Users/szhang3/Downloads/cryosparc_P141_J36_001_volume_map.mrc
Opened cryosparc_P141_J36_001_volume_map.mrc as #17, grid size 256,256,256,
pixel 2, shown at level 0.0693, step 1, values float32
> volume #17 level 0.8811
> select add #15
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.67099,-0.72968,0.13169,473.62,0.71538,-0.68378,-0.14376,225.89,0.19495,-0.0022474,0.98081,-36.493
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.67099,-0.72968,0.13169,487.59,0.71538,-0.68378,-0.14376,233.9,0.19495,-0.0022474,0.98081,-42.898
> view matrix models
> #15,-0.67099,-0.72968,0.13169,330.26,0.71538,-0.68378,-0.14376,144.25,0.19495,-0.0022474,0.98081,-13.741
> close #15
> select add #17
2 models selected
> view matrix models #17,1,0,0,-161.53,0,1,0,-11.067,0,0,1,-72.622
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.99923,0.018727,0.034358,-174.46,-0.019852,0.99927,0.032701,-14.052,-0.033721,-0.033358,0.99887,-55.745
> view matrix models
> #17,0.75605,0.60226,0.25627,-305.59,-0.23619,-0.1141,0.96498,68.361,0.61041,-0.79011,0.055978,195.39
> view matrix models
> #17,-0.087447,0.95716,0.27604,-176.32,0.15033,-0.26125,0.95349,6.0868,0.98476,0.12488,-0.12105,-72.494
> volume #17 level 1.058
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.087447,0.95716,0.27604,-67.343,0.15033,-0.26125,0.95349,12.984,0.98476,0.12488,-0.12105,-54.225
> view matrix models
> #17,-0.087447,0.95716,0.27604,-78.242,0.15033,-0.26125,0.95349,23.618,0.98476,0.12488,-0.12105,-28.93
> view matrix models
> #17,-0.087447,0.95716,0.27604,-78.441,0.15033,-0.26125,0.95349,24.409,0.98476,0.12488,-0.12105,-32.037
> show #!8 models
> ui tool show "Fit in Map"
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points
correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04
steps = 260, shift = 12.3, angle = 56 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.70324932 0.68336034 0.19610977 -193.58828243
-0.22024758 -0.05286234 0.97401056 49.89143717
0.67596701 -0.72816497 0.11333305 212.37654719
Axis -0.85709001 -0.24162070 -0.45499028
Axis point 0.00000000 175.75273055 124.55920872
Rotation angle (degrees) 96.78476794
Shift along axis 57.23851454
> transparency #17 50
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.9628,0.038849,0.2674,-126.46,-0.2702,0.13329,0.95353,23.314,0.0014013,-0.99031,0.13883,442.49
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points
correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04
steps = 204, shift = 15.3, angle = 42.5 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.70318709 0.68336267 0.19632468 -193.61262830
-0.22050568 -0.05290549 0.97394982 49.97965908
0.67594760 -0.72815964 0.11348290 212.35349781
Axis -0.85705446 -0.24150208 -0.45512020
Axis point 0.00000000 175.78346196 124.52896371
Rotation angle (degrees) 96.78348511
Shift along axis 57.22000862
> view matrix models
> #17,0.68912,0.63077,0.35672,-217.8,-0.40196,-0.076857,0.91242,117.31,0.60295,-0.77216,0.20058,219.93
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.68912,0.63077,0.35672,-190.71,-0.40196,-0.076857,0.91242,116.87,0.60295,-0.77216,0.20058,145.6
> view matrix models
> #17,0.68912,0.63077,0.35672,-190.77,-0.40196,-0.076857,0.91242,115.14,0.60295,-0.77216,0.20058,150.93
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.92014,0.31176,0.23695,-145.26,-0.22946,-0.061074,0.9714,52.068,0.31731,-0.9482,0.015339,312.65
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.92014,0.31176,0.23695,-167.69,-0.22946,-0.061074,0.9714,55.779,0.31731,-0.9482,0.015339,389.3
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points
correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04
steps = 136, shift = 6.81, angle = 25 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.70317534 0.68336839 0.19634684 -193.61854025
-0.22051976 -0.05292473 0.97394559 49.98975812
0.67595523 -0.72815288 0.11348086 212.34915105
Axis -0.85705062 -0.24149523 -0.45513107
Axis point 0.00000000 175.78569670 124.52495634
Rotation angle (degrees) 96.78443776
Shift along axis 57.22190560
> hide #!13 models
> hide #!16 models
> hide #!21 models
> view matrix models
> #17,0.70318,0.68337,0.19635,-194.4,-0.22052,-0.052925,0.97395,49.39,0.67596,-0.72815,0.11348,212.42
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.70318,0.68337,0.19635,-155.24,-0.22052,-0.052925,0.97395,42.132,0.67596,-0.72815,0.11348,202.16
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.8757,-0.44406,0.18964,68.194,-0.11865,0.18281,0.97596,-40.42,-0.46805,-0.87715,0.10739,534.82
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.8757,-0.44406,0.18964,50.163,-0.11865,0.18281,0.97596,-35.908,-0.46805,-0.87715,0.10739,539.61
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.94068,-0.31789,0.11859,21.277,-0.21114,-0.27486,0.93801,105.63,-0.26559,-0.90741,-0.32568,602.49
> view matrix models
> #17,0.91479,-0.33946,0.21892,8.0263,-0.17628,0.15214,0.97251,-12.894,-0.36344,-0.92824,0.079335,531.62
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.91479,-0.33946,0.21892,10.097,-0.17628,0.15214,0.97251,-18.102,-0.36344,-0.92824,0.079335,539.07
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points
correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04
steps = 252, shift = 4.47, angle = 55.9 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.24029116 -0.95069509 0.19605868 343.29956128
0.06441283 0.21714764 0.97401124 -92.11385375
-0.96856138 -0.22141760 0.11341562 503.63433465
Axis -0.61196839 0.59619664 0.51965783
Axis point 0.00000000 453.19259214 456.80776908
Rotation angle (degrees) 102.39046528
Shift along axis -3.28892408
> hide #!17 models
> show #!17 models
> hide #!8 models
> show #!12 models
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 56
shifted from previous position = 2.1
rotated from previous position = 3.55 degrees
atoms outside contour = 220, contour level = 1.0576
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75383878 -0.14056332 0.64184815 274.61567558
-0.18599955 0.98254436 -0.00327799 274.55087929
-0.63018352 -0.12185454 -0.76682476 264.50115086
Axis -0.09275720 0.99505418 -0.03554275
Axis point 199.66307778 0.00000000 83.28346891
Rotation angle (degrees) 140.26951543
Shift along axis 238.31932015
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 28
shifted from previous position = 0.00419
rotated from previous position = 0.0184 degrees
atoms outside contour = 220, contour level = 1.0576
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75392157 -0.14068518 0.64172419 274.62320626
-0.18624007 0.98249835 -0.00340870 274.56071911
-0.63001341 -0.12208466 -0.76692793 264.49389002
Axis -0.09285523 0.99504143 -0.03564336
Axis point 199.67028025 0.00000000 83.30375891
Rotation angle (degrees) 140.27991354
Shift along axis 238.27163930
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 44
shifted from previous position = 0.0467
rotated from previous position = 0.0218 degrees
atoms outside contour = 219, contour level = 1.0576
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75416077 -0.14066488 0.64144752 274.61545734
-0.18612770 0.98251977 -0.00337391 274.51436054
-0.62976028 -0.12193563 -0.76715950 264.48869026
Axis -0.09280514 0.99504815 -0.03558639
Axis point 199.62614812 0.00000000 83.32625385
Rotation angle (degrees) 140.30006211
Shift along axis 238.25708308
> select add #12
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 4 models selected
> view matrix models
> #12,-0.12774,-0.99178,0.0069335,230.82,-0.70239,0.085525,-0.70664,232.16,0.70024,-0.095134,-0.70754,200,#17,0.24029,-0.9507,0.19606,373.96,0.064413,0.21715,0.97401,-102.75,-0.96856,-0.22142,0.11342,496.77
> volume #17 level 1.667
> transparency #17 0
> set bgColor black
> set bgColor transparent
> lighting soft
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.23171,-0.95771,-0.17057,238.69,-0.85195,0.28442,-0.43965,239.85,0.46957,0.04344,-0.88183,216.26,#17,0.20006,-0.89727,0.39355,325.97,0.32049,0.43951,0.83912,-190.75,-0.92589,-0.041744,0.37549,382.67
> select subtract #17
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected
> view matrix models
> #12,-0.29588,-0.93972,-0.17143,241.58,-0.81142,0.34195,-0.474,239.48,0.50404,-0.0011431,-0.86368,213.96
> undo
[Repeated 2 time(s)]
> select subtract #17
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected
> view matrix models
> #12,-0.56325,-0.80162,0.2004,248.86,-0.42383,0.072085,-0.90287,223.16,0.70931,-0.59348,-0.38035,188.05
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 104
shifted from previous position = 2.45
rotated from previous position = 35.3 degrees
atoms outside contour = 1010, contour level = 1.6665
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75394829 -0.14065966 0.64169840 274.63622876
-0.18631825 0.98248303 -0.00355089 274.55457993
-0.62995832 -0.12223731 -0.76694886 264.49003822
Axis -0.09286893 0.99503717 -0.03572662
Axis point 199.67752190 0.00000000 83.31477226
Rotation angle (degrees) 140.28273670
Shift along axis 238.23750442
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> view matrix models
> #12,-0.52284,-0.81851,0.23806,246.45,-0.53039,0.093748,-0.84255,227.05,0.66732,-0.56679,-0.48315,191.47
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 88
shifted from previous position = 2.18
rotated from previous position = 30.7 degrees
atoms outside contour = 1005, contour level = 1.6665
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75403314 -0.14065260 0.64160024 274.61373569
-0.18621483 0.98250296 -0.00346098 274.56128623
-0.62988733 -0.12208518 -0.76703139 264.48802707
Axis -0.09283314 0.99504304 -0.03565618
Axis point 199.64917664 0.00000000 83.31915691
Rotation angle (degrees) 140.28934834
Shift along axis 238.27640921
> undo
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 40
shifted from previous position = 0.0106
rotated from previous position = 0.00925 degrees
atoms outside contour = 1008, contour level = 1.6665
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75385541 -0.14064919 0.64180981 274.62420754
-0.18636811 0.98247339 -0.00360001 274.54912593
-0.63005472 -0.12232678 -0.76685540 264.49135574
Axis -0.09288504 0.99503418 -0.03576788
Axis point 199.68627639 0.00000000 83.31105650
Rotation angle (degrees) 140.27481543
Shift along axis 238.21699160
> transparency #17 50
> volume #17 level 1.113
> hide #!17 models
> select #12/A:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 13 residues, 1 model selected
> select up
3482 atoms, 3540 bonds, 449 residues, 1 model selected
> color sel purple
> show #!17 models
> select #17
2 models selected
> show #!21 models
> show #!8 models
> select add #12
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.12749,-0.99181,0.0072951,207.62,-0.70271,0.085135,-0.70637,237,0.69996,-0.095183,-0.70781,216.33,#17,0.24029,-0.9507,0.19606,350.79,0.064413,0.21715,0.97401,-97.929,-0.96856,-0.22142,0.11342,513.11
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.44166,-0.69451,-0.56798,202.21,-0.85766,-0.141,-0.49451,233.52,0.26335,0.70554,-0.65792,255.54,#17,-0.5998,-0.7626,0.24224,512.23,0.349,0.023089,0.93684,-116.45,-0.72003,0.64646,0.2523,209.06
> view matrix models
> #12,-0.14812,-0.9886,-0.02695,208.45,-0.77331,0.13277,-0.61997,240.44,0.61648,-0.070989,-0.78417,219.67,#17,0.23341,-0.94357,0.23492,341.27,0.16639,0.27679,0.94641,-131.57,-0.95804,-0.18181,0.22161,474.07
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.14812,-0.9886,-0.02695,195.41,-0.77331,0.13277,-0.61997,243.95,0.61648,-0.070989,-0.78417,213.98,#17,0.23341,-0.94357,0.23492,328.23,0.16639,0.27679,0.94641,-128.06,-0.95804,-0.18181,0.22161,468.38
> view matrix models
> #12,-0.14812,-0.9886,-0.02695,200,-0.77331,0.13277,-0.61997,242.57,0.61648,-0.070989,-0.78417,212.13,#17,0.23341,-0.94357,0.23492,332.82,0.16639,0.27679,0.94641,-129.44,-0.95804,-0.18181,0.22161,466.54
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 70472 points
correlation = 0.8345, correlation about mean = 0.7897, overlap = 2.012e+04
steps = 72, shift = 2.54, angle = 6.92 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.23853813 -0.95106427 0.19640853 343.75560813
0.06546134 0.21753365 0.97385518 -92.36495526
-0.96892433 -0.21944443 0.11414801 503.06545376
Axis -0.61092202 0.59660416 0.52042075
Axis point 0.00000000 453.78241748 457.42033457
Rotation angle (degrees) 102.40907999
Shift along axis -3.30748718
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 56
shifted from previous position = 2.28
rotated from previous position = 6.93 degrees
atoms outside contour = 242, contour level = 1.1129
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75396462 -0.14067447 0.64167596 274.62896663
-0.18642584 0.98246220 -0.00366406 274.53988973
-0.62990694 -0.12238755 -0.76696710 264.48653786
Axis -0.09290279 0.99503133 -0.03580108
Axis point 199.67717545 0.00000000 83.32700147
Rotation angle (degrees) 140.28522076
Shift along axis 238.19309194
> select clear
> volume #17 level 0.301
> select add #17
2 models selected
> select add #12
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 4 models selected
> view matrix models
> #12,-0.12627,-0.99198,0.0059101,199.6,-0.70335,0.085322,-0.70571,243.41,0.69954,-0.093263,-0.70848,207.98,#17,0.23854,-0.95106,0.19641,343.25,0.065461,0.21753,0.97386,-91.856,-0.96892,-0.21944,0.11415,504.13
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.41673,-0.81863,0.39519,213.89,-0.59279,-0.084849,-0.80087,234.48,0.68915,-0.56802,-0.44992,192.33,#17,0.68295,-0.72803,0.059594,210.45,-0.055017,0.030085,0.99803,-22.64,-0.72839,-0.68488,-0.019508,585.55
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.41673,-0.81863,0.39519,213.07,-0.59279,-0.084849,-0.80087,237.86,0.68915,-0.56802,-0.44992,195.1,#17,0.68295,-0.72803,0.059594,209.62,-0.055017,0.030085,0.99803,-19.257,-0.72839,-0.68488,-0.019508,588.33
> view matrix models
> #12,-0.41673,-0.81863,0.39519,212.7,-0.59279,-0.084849,-0.80087,240.04,0.68915,-0.56802,-0.44992,194.06,#17,0.68295,-0.72803,0.059594,209.26,-0.055017,0.030085,0.99803,-17.073,-0.72839,-0.68488,-0.019508,587.29
> view matrix models
> #12,-0.41673,-0.81863,0.39519,212.96,-0.59279,-0.084849,-0.80087,239.29,0.68915,-0.56802,-0.44992,194.14,#17,0.68295,-0.72803,0.059594,209.52,-0.055017,0.030085,0.99803,-17.827,-0.72839,-0.68488,-0.019508,587.37
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.41673,-0.81863,0.39519,207.51,-0.59279,-0.084849,-0.80087,241.56,0.68915,-0.56802,-0.44992,193.87,#17,0.68295,-0.72803,0.059594,204.07,-0.055017,0.030085,0.99803,-15.552,-0.72839,-0.68488,-0.019508,587.1
> view matrix models
> #12,-0.41673,-0.81863,0.39519,208.03,-0.59279,-0.084849,-0.80087,237.84,0.68915,-0.56802,-0.44992,194.9,#17,0.68295,-0.72803,0.059594,204.58,-0.055017,0.030085,0.99803,-19.274,-0.72839,-0.68488,-0.019508,588.13
> view matrix models
> #12,-0.41673,-0.81863,0.39519,208.14,-0.59279,-0.084849,-0.80087,238.22,0.68915,-0.56802,-0.44992,194.55,#17,0.68295,-0.72803,0.059594,204.69,-0.055017,0.030085,0.99803,-18.892,-0.72839,-0.68488,-0.019508,587.78
> view matrix models
> #12,-0.41673,-0.81863,0.39519,208.62,-0.59279,-0.084849,-0.80087,238.13,0.68915,-0.56802,-0.44992,193.1,#17,0.68295,-0.72803,0.059594,205.18,-0.055017,0.030085,0.99803,-18.982,-0.72839,-0.68488,-0.019508,586.33
> view matrix models
> #12,-0.41673,-0.81863,0.39519,209.58,-0.59279,-0.084849,-0.80087,237.17,0.68915,-0.56802,-0.44992,198.86,#17,0.68295,-0.72803,0.059594,206.14,-0.055017,0.030085,0.99803,-19.946,-0.72839,-0.68488,-0.019508,592.09
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.41673,-0.81863,0.39519,208.43,-0.59279,-0.084849,-0.80087,240.29,0.68915,-0.56802,-0.44992,198.81,#17,0.68295,-0.72803,0.059594,204.98,-0.055017,0.030085,0.99803,-16.823,-0.72839,-0.68488,-0.019508,592.04
> view matrix models
> #12,-0.41673,-0.81863,0.39519,207.24,-0.59279,-0.084849,-0.80087,240.66,0.68915,-0.56802,-0.44992,196.58,#17,0.68295,-0.72803,0.059594,203.79,-0.055017,0.030085,0.99803,-16.456,-0.72839,-0.68488,-0.019508,589.81
> view matrix models
> #12,-0.41673,-0.81863,0.39519,205.84,-0.59279,-0.084849,-0.80087,235.35,0.68915,-0.56802,-0.44992,195.4,#17,0.68295,-0.72803,0.059594,202.39,-0.055017,0.030085,0.99803,-21.763,-0.72839,-0.68488,-0.019508,588.63
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.46523,-0.82013,0.3331,207.05,-0.57607,-0.0052031,-0.81739,237.6,0.67209,-0.57216,-0.47003,195.7,#17,0.67988,-0.72023,0.13795,181.58,-0.089433,0.10528,0.99041,-28.692,-0.72785,-0.6857,0.0071625,581.95
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.46523,-0.82013,0.3331,211.47,-0.57607,-0.0052031,-0.81739,234.38,0.67209,-0.57216,-0.47003,197.34,#17,0.67988,-0.72023,0.13795,186,-0.089433,0.10528,0.99041,-31.911,-0.72785,-0.6857,0.0071625,583.58
> view matrix models
> #12,-0.46523,-0.82013,0.3331,211.51,-0.57607,-0.0052031,-0.81739,234.73,0.67209,-0.57216,-0.47003,198.33,#17,0.67988,-0.72023,0.13795,186.04,-0.089433,0.10528,0.99041,-31.566,-0.72785,-0.6857,0.0071625,584.58
> view matrix models
> #12,-0.46523,-0.82013,0.3331,211.43,-0.57607,-0.0052031,-0.81739,234.73,0.67209,-0.57216,-0.47003,199.56,#17,0.67988,-0.72023,0.13795,185.97,-0.089433,0.10528,0.99041,-31.558,-0.72785,-0.6857,0.0071625,585.8
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.48108,-0.80208,0.35386,212.51,-0.64197,0.047429,-0.76526,238.39,0.59702,-0.59532,-0.53773,200.73,#17,0.70262,-0.69963,0.1298,177.29,-0.013704,0.16908,0.98551,-64.92,-0.71144,-0.69421,0.10921,557.81
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.48108,-0.80208,0.35386,211.69,-0.64197,0.047429,-0.76526,237.5,0.59702,-0.59532,-0.53773,202.7,#17,0.70262,-0.69963,0.1298,176.47,-0.013704,0.16908,0.98551,-65.804,-0.71144,-0.69421,0.10921,559.79
> view matrix models
> #12,-0.48108,-0.80208,0.35386,212.03,-0.64197,0.047429,-0.76526,236.16,0.59702,-0.59532,-0.53773,201.37,#17,0.70262,-0.69963,0.1298,176.81,-0.013704,0.16908,0.98551,-67.15,-0.71144,-0.69421,0.10921,558.46
> view matrix models
> #12,-0.48108,-0.80208,0.35386,210.74,-0.64197,0.047429,-0.76526,237.81,0.59702,-0.59532,-0.53773,205.39,#17,0.70262,-0.69963,0.1298,175.53,-0.013704,0.16908,0.98551,-65.5,-0.71144,-0.69421,0.10921,562.47
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points
correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04
steps = 176, shift = 3.59, angle = 29.8 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.26333938 -0.94460316 0.19590110 335.87494626
0.05857854 0.21835133 0.97411049 -90.92679362
-0.96292311 -0.24504605 0.11283398 508.38801880
Axis -0.62250579 0.59169989 0.51222825
Axis point 0.00000000 447.45056315 450.88479824
Rotation angle (degrees) 101.69709572
Shift along axis -2.47476769
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points
correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04
steps = 24, shift = 0.0114, angle = 0.0459 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.26266838 -0.94479741 0.19586519 336.09755618
0.05898515 0.21833646 0.97408928 -91.02138639
-0.96308154 -0.24430932 0.11307910 508.18910564
Axis -0.62214780 0.59179004 0.51255895
Axis point 0.00000000 447.61634049 451.12147224
Rotation angle (degrees) 101.70999009
Shift along axis -2.49103089
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points
correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04
steps = 24, shift = 0.00519, angle = 0.00771 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.26255870 -0.94483912 0.19581103 336.14644425
0.05903895 0.21828099 0.97409846 -91.02298534
-0.96310816 -0.24419755 0.11309389 508.16796837
Axis -0.62210531 0.59178539 0.51261588
Axis point 0.00000000 447.63086447 451.15689773
Rotation angle (degrees) 101.71438944
Shift along axis -2.48959114
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points
correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04
steps = 24, shift = 0.000512, angle = 0.00128 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.26253816 -0.94484341 0.19581785 336.15163822
0.05904075 0.21828599 0.97409723 -91.02458096
-0.96311365 -0.24417646 0.11309267 508.16428247
Axis -0.62209501 0.59179273 0.51261990
Axis point 0.00000000 447.63777500 451.16158673
Rotation angle (degrees) 101.71487962
Shift along axis -2.49081979
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.48108,-0.80208,0.35386,209.08,-0.64197,0.047429,-0.76526,234.23,0.59702,-0.59532,-0.53773,204.69,#17,0.26254,-0.94484,0.19582,334.28,0.059041,0.21829,0.9741,-95.231,-0.96311,-0.24418,0.11309,507.5
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points
correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04
steps = 56, shift = 4, angle = 0.0202 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.26243896 -0.94484804 0.19592848 336.12597123
0.05870710 0.21830347 0.97411347 -90.93814216
-0.96316108 -0.24414293 0.11276062 508.21187058
Axis -0.62211346 0.59189939 0.51247435
Axis point 0.00000000 447.64140705 451.06093433
Rotation angle (degrees) 101.72698571
Shift along axis -2.48917384
> volume #17 level 0.7131
> volume #17 level 0.9161
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 82019 points
correlation = 0.8223, correlation about mean = 0.7974, overlap = 2.027e+04
steps = 48, shift = 0.136, angle = 1 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.24597805 -0.94908637 0.19679903 341.20213079
0.06301258 0.21826572 0.97385290 -92.10297104
-0.96722500 -0.22714562 0.11349296 504.71777770
Axis -0.61434813 0.59543452 0.51772011
Axis point 0.00000000 451.89119580 455.38995867
Rotation angle (degrees) 102.18867732
Shift along axis -3.15563373
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.14478,-0.97394,-0.17459,197.38,-0.74565,0.0085955,-0.66629,233.93,0.65042,0.22665,-0.72497,231.5,#17,-0.57574,-0.79053,0.20875,512.98,0.17985,0.12661,0.97551,-101.72,-0.7976,0.59919,0.069283,277.02
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.14478,-0.97394,-0.17459,188.82,-0.74565,0.0085955,-0.66629,234.68,0.65042,0.22665,-0.72497,213.76,#17,-0.57574,-0.79053,0.20875,504.42,0.17985,0.12661,0.97551,-100.97,-0.7976,0.59919,0.069283,259.29
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 82019 points
correlation = 0.8223, correlation about mean = 0.7974, overlap = 2.027e+04
steps = 244, shift = 3.92, angle = 50.1 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.24595697 -0.94915233 0.19650703 341.29093539
0.06298376 0.21795680 0.97392396 -92.03239153
-0.96723224 -0.22716664 0.11338917 504.74584026
Axis -0.61442468 0.59531740 0.51776394
Axis point 0.00000000 451.81499078 455.37215285
Rotation angle (degrees) 102.20139130
Shift along axis -3.14686612
> fitmap #17 inMap #8
Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 82019 points
correlation = 0.8223, correlation about mean = 0.7974, overlap = 2.027e+04
steps = 28, shift = 0.02, angle = 0.00572 degrees
Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.24596145 -0.94915694 0.19647915 341.31667969
0.06308318 0.21795208 0.97391858 -92.05723234
-0.96722462 -0.22715189 0.11348365 504.72349239
Axis -0.61440799 0.59529304 0.51781176
Axis point 0.00000000 451.82706073 455.40596199
Rotation angle (degrees) 102.19862946
Shift along axis -3.15696319
> fitmap #12 inMap #17
Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms
average map value = 2.45, steps = 76
shifted from previous position = 8.36
rotated from previous position = 19.6 degrees
atoms outside contour = 176, contour level = 0.9161
Position of 4zyp_Mota_AM14.pdb (#12) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.75414553 -0.14067198 0.64146388 274.60252920
-0.18620159 0.98250551 -0.00344853 274.54253886
-0.62975669 -0.12204229 -0.76714548 264.48668317
Axis -0.09282891 0.99504408 -0.03563817
Axis point 199.62736777 0.00000000 83.33289175
Rotation angle (degrees) 140.29938978
Shift along axis 238.26505255
> hide #!8 models
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
Chain information for RSVAmono_MEDI_Mota_model.pdb #15
---
Chain | Description
B | No description available
C | No description available
D | No description available
H | No description available
L | No description available
> hide sel atoms
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select subtract #17
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> select #15/L:199@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 7 residues, 1 model selected
> select up
1619 atoms, 1654 bonds, 211 residues, 1 model selected
> select up
10085 atoms, 10311 bonds, 1314 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #!17 models
> select add #12/B:506
10093 atoms, 10318 bonds, 1315 residues, 2 models selected
Drag select of 492 residues, 2 pseudobonds
> select up
4059 atoms, 4147 bonds, 2 pseudobonds, 545 residues, 4 models selected
> select up
6474 atoms, 6642 bonds, 2 pseudobonds, 848 residues, 4 models selected
> select up
20170 atoms, 20622 bonds, 6 pseudobonds, 2628 residues, 4 models selected
> ui tool show "Fit in Map"
> ui tool show Matchmaker
> matchmaker #!15 & sel to #21 & 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 mono_MEDI_Mota, chain B (#21) with RSVAmono_MEDI_Mota_model.pdb,
chain B (#15), sequence alignment score = 2486.8
RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
0.000)
> select clear
> hide #!12 models
> show #!12 models
> hide #!15 models
> show #!15 models
> hide #!21 models
> hide #!12 models
Drag select of 320 residues, 1 pseudobonds
> select up
2829 atoms, 2887 bonds, 1 pseudobond, 375 residues, 2 models selected
> select up
6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 2 models selected
> delete atoms (#!15 & sel)
> delete bonds (#!15 & sel)
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!17 models
> show #!12 models
> select add #15
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> select subtract #15
Nothing selected
> select add #15
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> view matrix models
> #15,0.99832,0.042098,0.039812,-8.9067,-0.039991,0.99783,-0.052307,33.148,-0.041927,0.050627,0.99784,-1.8934
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.51669,0.60051,0.61026,-166.8,-0.25736,0.78875,-0.55824,211.35,-0.81657,0.13138,0.56209,186.36
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.51669,0.60051,0.61026,-184.23,-0.25736,0.78875,-0.55824,233.93,-0.81657,0.13138,0.56209,217.32
> view matrix models
> #15,0.51669,0.60051,0.61026,-163.46,-0.25736,0.78875,-0.55824,237.06,-0.81657,0.13138,0.56209,234.95
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.45704,0.88924,0.019064,-84.944,0.22467,-0.094679,-0.96982,423.33,-0.86061,0.44753,-0.24306,351.24
> view matrix models
> #15,0.34695,0.69419,0.63065,-161.22,0.6988,0.25715,-0.6675,223.99,-0.62555,0.67228,-0.39588,306.83
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.34695,0.69419,0.63065,-155.21,0.6988,0.25715,-0.6675,218.39,-0.62555,0.67228,-0.39588,321.09
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.35664,0.91127,0.2059,-108.2,0.33944,0.078942,-0.93731,361.19,-0.8704,0.40417,-0.28117,383.24
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.35664,0.91127,0.2059,-111.9,0.33944,0.078942,-0.93731,356.36,-0.8704,0.40417,-0.28117,377.47
> fitmap #15 inMap #17
Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms
average map value = 2.504, steps = 264
shifted from previous position = 70.8
rotated from previous position = 19 degrees
atoms outside contour = 160, contour level = 0.9161
Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.95762749 -0.28800913 -0.00059252 162.69514121
-0.24938915 -0.82818387 -0.50191287 549.31419915
0.14406477 0.48079333 -0.86491799 288.76390270
Axis 0.98859165 -0.14552365 0.03885127
Axis point 0.00000000 248.24855247 216.92170178
Rotation angle (degrees) 150.19674124
Shift along axis 92.11969663
> view matrix models
> #15,0.50055,0.8097,0.30631,-112.84,0.14636,0.26958,-0.95179,314.72,-0.85324,0.52126,0.01643,309.15
> view matrix models
> #15,0.50055,0.8097,0.30631,-117.37,0.14636,0.26958,-0.95179,326.66,-0.85324,0.52126,0.01643,316.8
> view matrix models
> #15,0.50055,0.8097,0.30631,-126.2,0.14636,0.26958,-0.95179,337.95,-0.85324,0.52126,0.01643,293.29
> view matrix models
> #15,0.50055,0.8097,0.30631,-128.98,0.14636,0.26958,-0.95179,349.02,-0.85324,0.52126,0.01643,294.16
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.69146,0.71483,-0.10444,-51.479,0.10539,-0.24283,-0.96433,455.36,-0.71469,0.65579,-0.24324,303.46
> fitmap #15 inMap #17
Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms
average map value = 2.547, steps = 832
shifted from previous position = 62.9
rotated from previous position = 108 degrees
atoms outside contour = 47, contour level = 0.9161
Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.29462335 -0.71397673 0.63516480 215.41870644
0.67519967 -0.31482104 -0.66707805 366.69507471
0.67624144 0.62539983 0.38932322 -72.28107957
Axis 0.68100675 -0.02164329 0.73195722
Axis point -40.28268173 259.62048826 0.00000000
Rotation angle (degrees) 108.38721116
Shift along axis 85.85844847
> undo
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.19483,0.82204,0.53506,-135.71,-0.049845,0.5531,-0.83162,297.73,-0.97957,0.13535,0.14873,358.02
> view matrix models
> #15,0.57305,0.80444,-0.15651,-40.524,0.3457,-0.41044,-0.84382,427.27,-0.74304,0.42945,-0.5133,407.86
> volume #17 level 0.8361
> view matrix models
> #15,0.66079,0.69021,-0.2949,-2.0843,0.32345,-0.6164,-0.71793,443.16,-0.6773,0.37902,-0.63056,432.82
> view matrix models
> #15,0.63533,0.77115,-0.040903,-67.588,0.23026,-0.23973,-0.94314,432.32,-0.73711,0.58979,-0.32988,337.61
> view matrix models
> #15,0.52932,0.84143,0.10873,-97.387,0.33037,-0.08637,-0.93989,387.95,-0.78146,0.53342,-0.3237,353.45
> view matrix models
> #15,0.71456,0.69799,-0.047018,-63.735,0.33911,-0.40437,-0.84941,428.25,-0.61189,0.59101,-0.52564,360.76
> view matrix models
> #15,0.54901,-0.30078,0.77982,-24.158,-0.83521,-0.16191,0.52556,260.2,-0.031821,-0.93985,-0.3401,530.19
> view matrix models
> #15,0.78148,-0.31664,0.53761,-3.3674,-0.62358,-0.36763,0.68993,234.24,-0.020819,-0.87441,-0.48475,546.71
> fitmap #15 inMap #17
Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms
average map value = 2.572, steps = 256
shifted from previous position = 69.5
rotated from previous position = 12 degrees
atoms outside contour = 27, contour level = 0.83613
Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.23981198 0.83025195 0.50316192 -49.55829511
-0.91635012 0.36474602 -0.16511455 346.76529763
-0.32061298 -0.42147603 0.84827194 165.74602048
Axis -0.13159822 0.42286896 -0.89658449
Axis point 205.19400853 246.84698063 0.00000000
Rotation angle (degrees) 76.91390262
Shift along axis 4.55275294
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.54901,-0.30078,0.77982,-26.134,-0.83521,-0.16191,0.52556,259.46,-0.031821,-0.93985,-0.3401,529.99
> view matrix models
> #15,0.54901,-0.30078,0.77982,-27.017,-0.83521,-0.16191,0.52556,261.44,-0.031821,-0.93985,-0.3401,526.93
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.5036,-0.58422,0.63646,63.936,-0.79588,-0.027129,0.60485,213.29,-0.33609,-0.81114,-0.47863,575.46
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.5036,-0.58422,0.63646,63.014,-0.79588,-0.027129,0.60485,215.86,-0.33609,-0.81114,-0.47863,574.16
> fitmap #15 inMap #17
Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms
average map value = 2.572, steps = 256
shifted from previous position = 69.6
rotated from previous position = 31.8 degrees
atoms outside contour = 27, contour level = 0.83613
Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.24068380 0.83093813 0.50161054 -49.46780136
-0.91608696 0.36524164 -0.16547881 346.71221958
-0.32071170 -0.41969081 0.84911933 165.23344332
Axis -0.13052942 0.42223515 -0.89703933
Axis point 205.48317396 246.57687629 0.00000000
Rotation angle (degrees) 76.84875230
Shift along axis 4.63019080
> undo
> view matrix models
> #15,0.5036,-0.58422,0.63646,63.883,-0.79588,-0.027129,0.60485,213.31,-0.33609,-0.81114,-0.47863,575.5
> ui mousemode right zoom
> select clear
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
Chain information for RSVAmono_MEDI_Mota_model.pdb #18
---
Chain | Description
B | No description available
C | No description available
D | No description available
H | No description available
L | No description available
> select #18/L:160@CG
1 atom, 1 residue, 1 model selected
> select #18/D:66@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> select up
1042 atoms, 1072 bonds, 134 residues, 1 model selected
> select up
1049 atoms, 1078 bonds, 135 residues, 1 model selected
> select up
1626 atoms, 1671 bonds, 213 residues, 1 model selected
> select up
10085 atoms, 10311 bonds, 1314 residues, 1 model selected
> select up
40701 atoms, 41562 bonds, 5285 residues, 31 models selected
> select down
10085 atoms, 10311 bonds, 1314 residues, 1 model selected
> select down
1626 atoms, 1671 bonds, 213 residues, 1 model selected
> select up
10085 atoms, 10311 bonds, 1314 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!12 models
> hide #!15 models
> hide #!17 models
Drag select of 412 residues, 2 pseudobonds
> select up
3879 atoms, 3948 bonds, 2 pseudobonds, 504 residues, 2 models selected
> select up
6719 atoms, 6853 bonds, 2 pseudobonds, 877 residues, 2 models selected
> delete atoms (#!18 & sel)
> delete bonds (#!18 & sel)
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
Chain information for RSVAmono_MEDI_Mota_model.pdb #19
---
Chain | Description
B | No description available
C | No description available
D | No description available
H | No description available
L | No description available
> hide #!18-19 atoms
> show #!18-19 cartoons
> select clear
Drag select of 357 residues, 1 pseudobonds
> select up
3498 atoms, 3559 bonds, 1 pseudobond, 451 residues, 2 models selected
> select up
6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 2 models selected
> delete atoms (#!19 & sel)
> delete bonds (#!19 & sel)
> show #!17 models
> show #!15 models
> show #!12 models
> select add #18
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.55429,0.10497,-0.82568,218.75,-0.57303,0.7676,-0.28709,187.56,0.60366,0.63227,0.48563,-98.776
> view matrix models
> #18,0.63305,0.033195,-0.7734,210.06,-0.47624,0.80434,-0.35529,181.04,0.61028,0.59324,0.525,-100.61
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.63305,0.033195,-0.7734,249.06,-0.47624,0.80434,-0.35529,224.92,0.61028,0.59324,0.525,-155.92
> view matrix models
> #18,0.63305,0.033195,-0.7734,257.89,-0.47624,0.80434,-0.35529,218.35,0.61028,0.59324,0.525,-152.02
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.33306,0.54093,0.77231,-26.862,-0.60108,-0.75288,0.26811,401.68,0.72648,-0.37492,0.57589,5.265
> view matrix models
> #18,-0.37042,0.91343,0.16865,35.097,-0.73583,-0.39937,0.54686,294.65,0.56687,0.078465,0.82006,-109.93
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.37042,0.91343,0.16865,34.18,-0.73583,-0.39937,0.54686,292.61,0.56687,0.078465,0.82006,-109.39
> view matrix models
> #18,-0.37042,0.91343,0.16865,34.659,-0.73583,-0.39937,0.54686,291.39,0.56687,0.078465,0.82006,-108.73
> select subtract #18
Nothing selected
> select add #19
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> view matrix models #19,1,0,0,0.048033,0,1,0,-0.097133,0,0,1,0.18177
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.16657,0.081137,0.98269,-103.31,0.72911,-0.68107,-0.067351,230.04,0.66382,0.72771,-0.1726,13.746
> view matrix models
> #19,-0.73965,-0.18703,0.64648,149.43,0.38059,-0.90849,0.1726,272.86,0.55504,0.37371,0.74315,-96.714
> view matrix models
> #19,0.21338,0.96846,0.12869,-98.777,-0.83027,0.11033,0.54634,173.66,0.51491,-0.22343,0.82762,5.1646
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.21338,0.96846,0.12869,16.157,-0.83027,0.11033,0.54634,172.66,0.51491,-0.22343,0.82762,-8.909
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.74953,-0.64739,-0.13817,519.6,-0.45452,0.35155,0.81843,14.989,-0.48127,0.67623,-0.55775,255.78
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.74953,-0.64739,-0.13817,545.74,-0.45452,0.35155,0.81843,29.773,-0.48127,0.67623,-0.55775,294.13
> view matrix models
> #19,-0.74953,-0.64739,-0.13817,538.74,-0.45452,0.35155,0.81843,16.554,-0.48127,0.67623,-0.55775,297.27
> view matrix models
> #19,-0.74953,-0.64739,-0.13817,539.4,-0.45452,0.35155,0.81843,20.659,-0.48127,0.67623,-0.55775,302.02
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.46575,-0.80685,-0.36342,576.62,-0.7528,0.14538,0.642,140.26,-0.46516,0.57259,-0.6751,344.3
> view matrix models
> #19,-0.37055,-0.75396,-0.54243,590.69,-0.82322,-0.0038459,0.56771,194.59,-0.43012,0.65691,-0.61925,311.35
> view matrix models
> #19,-0.43822,-0.65378,-0.61687,597.05,-0.57456,-0.32404,0.75158,181.02,-0.69126,0.68379,-0.23364,262.25
> view matrix models
> #19,-0.58763,-0.57197,-0.57231,593.52,-0.52216,-0.27225,0.80823,151.61,-0.6181,0.77377,-0.13868,214.46
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.58763,-0.57197,-0.57231,585.56,-0.52216,-0.27225,0.80823,156.28,-0.6181,0.77377,-0.13868,221.39
> view matrix models
> #19,-0.58763,-0.57197,-0.57231,583.23,-0.52216,-0.27225,0.80823,159.15,-0.6181,0.77377,-0.13868,217.39
> select subtract #19
Nothing selected
> select add #19
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> select add #18
6732 atoms, 6916 bonds, 2 pseudobonds, 874 residues, 4 models selected
> view matrix models
> #18,-0.37042,0.91343,0.16865,41.333,-0.73583,-0.39937,0.54686,295.03,0.56687,0.078465,0.82006,-107.94,#19,-0.58763,-0.57197,-0.57231,589.91,-0.52216,-0.27225,0.80823,162.78,-0.6181,0.77377,-0.13868,218.18
> undo
> select subtract #19
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> view matrix models
> #18,-0.37042,0.91343,0.16865,42.288,-0.73583,-0.39937,0.54686,295.35,0.56687,0.078465,0.82006,-107.51
> view matrix models
> #18,-0.37042,0.91343,0.16865,41.12,-0.73583,-0.39937,0.54686,294.52,0.56687,0.078465,0.82006,-107.34
> select clear
> color #17 #ebebebff models
> transparency #17 50
> set bgColor white
> set bgColor #ffffff00
> volume #17 level 1.039
> color #15 silver
> color #15 darkgrey
> select clear
> color #15 #fffb00ff
> color #19 #fffb00ff
> color #20 #fffb00ff
> select clear
> color #18 #fffb00ff
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!18 models
> hide #!19 models
> show #!19 models
> show #!18 models
> show #!15 models
> combine #15,18,19
Remapping chain ID 'A' in RSVAmono_MEDI_Mota_model.pdb #18 to 'B'
Remapping chain ID 'C' in RSVAmono_MEDI_Mota_model.pdb #18 to 'E'
Remapping chain ID 'D' in RSVAmono_MEDI_Mota_model.pdb #18 to 'G'
Remapping chain ID 'F' in RSVAmono_MEDI_Mota_model.pdb #18 to 'H'
Remapping chain ID 'I' in RSVAmono_MEDI_Mota_model.pdb #18 to 'J'
Remapping chain ID 'A' in RSVAmono_MEDI_Mota_model.pdb #19 to 'K'
Remapping chain ID 'C' in RSVAmono_MEDI_Mota_model.pdb #19 to 'L'
Remapping chain ID 'D' in RSVAmono_MEDI_Mota_model.pdb #19 to 'M'
Remapping chain ID 'F' in RSVAmono_MEDI_Mota_model.pdb #19 to 'N'
Remapping chain ID 'I' in RSVAmono_MEDI_Mota_model.pdb #19 to 'O'
> close #18-19
> close #15
> hide #!12 models
> show #!12 models
> combine #12,22
Remapping chain ID 'A' in combination #22 to 'P'
Remapping chain ID 'B' in combination #22 to 'Q'
Remapping chain ID 'C' in combination #22 to 'R'
> hide #!22 models
> hide #!15 models
> close #15
> show #!22 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!22 models
> show #!22 models
> combine #12,22
Remapping chain ID 'A' in combination #22 to 'P'
Remapping chain ID 'B' in combination #22 to 'Q'
Remapping chain ID 'C' in combination #22 to 'R'
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!15 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!15 models
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102_RSVA-PreF-trimer.pdb"
> models #15 relModel #17
> hide #!17 models
> hide #!15 models
> close #17
> close #15
> show #!22 models
> close #22
> show #!21 models
> show #!20 models
> hide #!20 models
> show #!16 models
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
Chain information for RSVAmono_MEDI_Mota_model.pdb #15
---
Chain | Description
B | No description available
C | No description available
D | No description available
H | No description available
L | No description available
> hide #!15,21 atoms
> show #!15,21 cartoons
> hide #!15 models
> show #!15 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!16 models
Drag select of 200 residues
> select up
2210 atoms, 2244 bonds, 279 residues, 1 model selected
> select up
6145 atoms, 6265 bonds, 799 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 78 residues
> select up
3940 atoms, 4046 bonds, 515 residues, 1 model selected
> select up
31190 atoms, 31839 bonds, 4049 residues, 28 models selected
> select down
3940 atoms, 4046 bonds, 515 residues, 1 model selected
> select down
574 atoms, 78 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!16 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!15 models
> show #!15 models
> select add #15
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> view matrix models #15,1,0,0,23.361,0,1,0,53.548,0,0,1,-12.247
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.61272,0.4682,0.63668,31.486,-0.14783,0.7235,-0.67431,270.22,-0.77635,-0.50729,-0.37409,486.94
> view matrix models
> #15,-0.60749,0.46833,0.64158,29.673,-0.15035,0.7253,-0.67181,269.71,-0.77997,-0.50458,-0.3702,486.12
> view matrix models
> #15,-0.26951,0.7708,0.57726,-63.103,-0.78375,0.17274,-0.59657,450.43,-0.55956,-0.61321,0.55756,278.91
> view matrix models
> #15,-0.23628,0.83096,0.50367,-63.802,-0.77933,0.14753,-0.609,457.23,-0.58036,-0.53642,0.61273,255.58
> view matrix models
> #15,0.48556,0.41166,-0.77121,181.95,-0.80982,-0.12048,-0.57418,505.41,-0.32928,0.90334,0.27487,16.108
> view matrix models
> #15,0.8129,0.25728,-0.5225,111.7,0.16214,-0.96164,-0.22126,451.4,-0.55938,0.095142,-0.82343,435.77
> view matrix models
> #15,0.83049,0.32886,-0.44959,80.084,0.32753,-0.94115,-0.083402,394.52,-0.45056,-0.077992,-0.88933,467.09
> view matrix models
> #15,0.44192,0.70749,-0.55151,85.307,0.23191,-0.68401,-0.69163,487.85,-0.86656,0.17775,-0.46635,388.7
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.44192,0.70749,-0.55151,88.228,0.23191,-0.68401,-0.69163,489.07,-0.86656,0.17775,-0.46635,457.3
> view matrix models
> #15,0.44192,0.70749,-0.55151,105.93,0.23191,-0.68401,-0.69163,490.02,-0.86656,0.17775,-0.46635,444.96
> view matrix models
> #15,0.44192,0.70749,-0.55151,112.31,0.23191,-0.68401,-0.69163,495.87,-0.86656,0.17775,-0.46635,448.4
> fitmap #15 inMap #16
Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled (#16) using
3366 atoms
average map value = 1.865, steps = 140
shifted from previous position = 12.4
rotated from previous position = 30.1 degrees
atoms outside contour = 187, contour level = 1.1617
Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled (#16)
coordinates:
Matrix rotation and translation
-0.05745200 0.79150272 -0.60845928 185.43737272
0.35509446 -0.55341035 -0.75342212 457.08323274
-0.93306333 -0.25934613 -0.24926369 501.42714965
Axis 0.67239520 0.44175836 -0.59391434
Axis point 0.00000000 94.22720794 395.50982080
Rotation angle (degrees) 158.44464219
Shift along axis 28.80276358
> select clear
> ui mousemode right zoom
> hide #!16 models
> show #!16 models
> hide #!16 models
> color #15 #0433ffff
> color #15 #00f900ff
> color #15 #5eaf88ff
> color #15 #00f900ff
> select add #15
3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected
> color (#!15 & sel) forest green
> show #!16 models
> select clear
> color #16 #a6ca8cff models
> color #16 #8ec9a4ff models
> color #16 #e6f1f7ff models
> transparency 50
> select clear
> undo
[Repeated 8 time(s)]
> show #!16 models
> transparency 50
> select clear
> combine #15,21
Remapping chain ID 'A' in mono_MEDI_Mota #21 to 'E'
Remapping chain ID 'C' in mono_MEDI_Mota #21 to 'G'
Remapping chain ID 'D' in mono_MEDI_Mota #21 to 'J'
Remapping chain ID 'F' in mono_MEDI_Mota #21 to 'K'
Remapping chain ID 'I' in mono_MEDI_Mota #21 to 'M'
> hide #!17 models
> hide #!15 models
> hide #!21 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/101/101_RSVA-
> mono_MEDI_Mota.pdb" models #17 relModel #16
> hide #!17 models
> show #!17 models
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc" models #16
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/101/101_RSVA-mono_MEDI_Mota.pdb
Chain information for 101_RSVA-mono_MEDI_Mota.pdb #18
---
Chain | Description
B | No description available
C G | No description available
D J | No description available
H | No description available
L | No description available
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc
Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #19, grid size
208,208,208, pixel 2, shown at level 0.0913, step 1, values float32
> volume #19 level 0.4148
> hide #!16 models
> hide #!17 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!19 models
Drag select of 128 atoms
> select up
13451 atoms, 13769 bonds, 1751 residues, 1 model selected
> select down
128 atoms, 12 residues, 1 model selected
> select add #18/A:601@CL
129 atoms, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!19 models
> hide #!18 atoms
> show #!18 cartoons
> hide #!19 models
> show #!19 models
> close #18-19
> show #!20 models
> show #!21 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!20 models
> hide #!21 models
> show #!12 models
Drag select of 9 residues
> select up
352 atoms, 352 bonds, 44 residues, 2 models selected
> select up
6964 atoms, 7080 bonds, 898 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!12 & sel to #17 & 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 combination, chain B (#17) with 4zyp_Mota_AM14.pdb, chain B (#12),
sequence alignment score = 2486.8
RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
0.000)
> select clear
> color #12 #d6d6d6ff
> color #12 silver
> color #12 darkgrey
> color #12 silver
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!17 models
> show #!12 models
> hide #!12 models
> show #!17 models
> show #!12 models
> select #17/B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 7 residues
> select up
61 atoms, 16 bonds, 7 residues, 2 models selected
> select up
363 atoms, 364 bonds, 42 residues, 2 models selected
> select up
10446 atoms, 10621 bonds, 1347 residues, 2 models selected
> select clear
Drag select of 4 residues
> select up
158 atoms, 158 bonds, 18 residues, 2 models selected
> select up
6964 atoms, 7080 bonds, 898 residues, 2 models selected
> color sel gray
> select clear
> hide #12.1 models
> hide #!17.1 models
> select clear
> show #!17.1 models
> select #12/C:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
80 atoms, 79 bonds, 10 residues, 1 model selected
> select up
3482 atoms, 3541 bonds, 449 residues, 1 model selected
> color sel hot pink
> select clear
> select #12/C:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
82 atoms, 84 bonds, 10 residues, 1 model selected
> select up
3482 atoms, 3541 bonds, 449 residues, 1 model selected
> color sel magenta
> color sel orange
> color sel hot pink
> select clear
Drag select of 125 residues
> view sel
> select clear
[Repeated 1 time(s)]
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/MAbs/101/101_trimer_monomer_3fabs.png" width 651 height 661
> supersample 3 transparentBackground true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie1.mp4
Movie saved to /Users/szhang3/Desktop/movie1.mp4
> show #!16 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie2.mp4
Movie saved to /Users/szhang3/Desktop/movie2.mp4
> lighting soft
> lighting simple
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/szhang3/Desktop/movie3.mp4
Movie saved to /Users/szhang3/Desktop/movie3.mp4
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
> true
> show #!21 models
> hide #!17 models
> show #!17 models
> close #21
> hide #!17 models
> show #!17 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!17 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> close #15
> show #!20 models
> hide #!20 models
> close #20
> show #!17 models
> show #!16 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!16 models
> hide #!17 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> select add #13
5 models selected
> view sel
Window position QRect(1795,566 600x300) outside any known screen, using
primary screen
No displayed objects specified.
> close #13
> show #!14 models
> show #!12 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> hide #!14 models
> show #!12 models
> show #!14 models
> show #!17 models
> hide #!14 models
> hide #!17 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!17 models
> hide #!17 models
> show #!14 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #!14 models
> close #14
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!12 models
> show #!16 models
> show #!17 models
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/102/102_RSVA-PreF-trimer.pdb
Chain information for 102_RSVA-PreF-trimer.pdb #13
---
Chain | Description
A B C | No description available
D G M | No description available
E L R | No description available
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/102/cryosparc_P141_J36_001_volume_map.mrc
Opened cryosparc_P141_J36_001_volume_map.mrc as #14, grid size 256,256,256,
pixel 2, shown at level 0.0693, step 1, values float32
> volume #14 level 0.7208
> volume #14 level 1.044
> transparency 50
> hide #!17 models
> show #!17 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!17 models
> show #!17 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select add #12
10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected
> select subtract #12
Nothing selected
> select add #13
20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 2 models selected
> color #13 #424242ff
> color #13 #00f900ff
> color #13 #008f00ff
> color #13 #919191ff
> color #13 #009193ff
> color #13 #4f8f00ff
> color #13 #9437ffff
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,556.84,0,1,0,181.23,0,0,1,-206.43
> view matrix models #13,1,0,0,513.32,0,1,0,205.36,0,0,1,-202.66
> view matrix models #13,1,0,0,503.7,0,1,0,238.02,0,0,1,-237.5
> view matrix models #13,1,0,0,501.73,0,1,0,236.59,0,0,1,-240.18
> ui mousemode right zoom
> hide #!12 models
> hide #!14 models
> show #!14 models
> hide #!16 models
> hide #!17 models
> ui tool show "Side View"
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.4947,0.047412,0.86777,-59.308,-0.29285,0.94921,0.11509,98.704,-0.81823,-0.31106,0.48346,-220.74
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.4947,0.047412,0.86777,-23.35,-0.29285,0.94921,0.11509,117.35,-0.81823,-0.31106,0.48346,-204.85
> fitmap #13 inMap #14
Fit molecule 102_RSVA-PreF-trimer.pdb (#13) to map
cryosparc_P141_J36_001_volume_map.mrc (#14) using 20544 atoms
average map value = 1.953, steps = 100
shifted from previous position = 14.8
rotated from previous position = 13.6 degrees
atoms outside contour = 2141, contour level = 1.0438
Position of 102_RSVA-PreF-trimer.pdb (#13) relative to
cryosparc_P141_J36_001_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.55034274 0.16955768 0.81754088 11.73024931
-0.19355143 0.97839830 -0.07262672 220.25650910
-0.81219501 -0.11826661 0.57127252 -254.99367436
Axis -0.02732403 0.97570255 -0.21738890
Axis point -177.74270461 0.00000000 -121.13339893
Rotation angle (degrees) 56.63252247
Shift along axis 270.01711300
> show #!16 models
> show #!12 models
> hide #!16 models
> select add #14
20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.1273,0.63314,0.7635,-79.993,-0.94959,-0.14454,0.27819,-160.39,0.28649,-0.76042,0.58283,46.734,#14,0.8016,0.53938,0.25789,-142.44,-0.31968,0.022173,0.94727,80.019,0.50522,-0.84177,0.1902,274.71
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.1273,0.63314,0.7635,-112.25,-0.94959,-0.14454,0.27819,-185.42,0.28649,-0.76042,0.58283,13.296,#14,0.8016,0.53938,0.25789,-174.7,-0.31968,0.022173,0.94727,54.989,0.50522,-0.84177,0.1902,241.28
> view matrix models
> #13,0.1273,0.63314,0.7635,-136.19,-0.94959,-0.14454,0.27819,-177.84,0.28649,-0.76042,0.58283,18.694,#14,0.8016,0.53938,0.25789,-198.63,-0.31968,0.022173,0.94727,62.577,0.50522,-0.84177,0.1902,246.67
> view matrix models
> #13,0.1273,0.63314,0.7635,-139.11,-0.94959,-0.14454,0.27819,-177.31,0.28649,-0.76042,0.58283,36.077,#14,0.8016,0.53938,0.25789,-201.55,-0.31968,0.022173,0.94727,63.1,0.50522,-0.84177,0.1902,264.06
> view matrix models
> #13,0.1273,0.63314,0.7635,-131.93,-0.94959,-0.14454,0.27819,-182.03,0.28649,-0.76042,0.58283,39.082,#14,0.8016,0.53938,0.25789,-194.37,-0.31968,0.022173,0.94727,58.381,0.50522,-0.84177,0.1902,267.06
> ui tool show Matchmaker
> matchmaker #!13 & sel to #12 & sel
No 'to' model specified
> select add #12
30990 atoms, 31616 bonds, 9 pseudobonds, 4005 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!13 & sel to #12 & 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 4zyp_Mota_AM14.pdb, chain A (#12) with 102_RSVA-PreF-trimer.pdb,
chain A (#13), sequence alignment score = 2489.2
RMSD between 449 pruned atom pairs is 0.001 angstroms; (across all 449 pairs:
0.001)
> ui tool show "Fit in Map"
> fitmap #16 inMap #8
Fit map P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 44648 points
correlation = 0.7033, correlation about mean = 0.2694, overlap = 9030
steps = 336, shift = 36.7, angle = 52.8 degrees
Position of P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc (#16) relative to
preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.63499761 -0.60502993 0.48032990 106.67366773
0.45142417 0.79518516 0.40484167 -149.98927774
-0.62689254 -0.04024096 0.77806581 168.17260938
Axis -0.27926224 0.69471464 0.66286060
Axis point 288.45766169 0.00000000 10.20458531
Rotation angle (degrees) 52.83414700
Shift along axis -22.51467756
> show #!8 models
> hide #!8 models
> show #!8 models
> fitmap #16 inMap #8
Fit map P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 44648 points
correlation = 0.7034, correlation about mean = 0.2698, overlap = 9030
steps = 48, shift = 0.0587, angle = 0.134 degrees
Position of P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc (#16) relative to
preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.63600736 -0.60429647 0.47991710 106.40988355
0.44966402 0.79563234 0.40592050 -150.05527072
-0.62713389 -0.04236698 0.77775840 168.73735361
Axis -0.28142708 0.69498735 0.66165806
Axis point 289.07522752 0.00000000 10.76828252
Rotation angle (degrees) 52.79281114
Shift along axis -22.58670798
> view matrix models
> #12,-0.18088,-0.9835,0.0018353,203.97,-0.71723,0.13063,-0.68448,241.88,0.67295,-0.12512,-0.72903,207.89,#13,0.046808,0.77485,0.63041,-92.939,-0.92342,-0.20709,0.32311,-192.36,0.38091,-0.59726,0.70583,3.4601,#14,0.8016,0.53938,0.25789,-194.43,-0.31968,0.022173,0.94727,58.108,0.50522,-0.84177,0.1902,267
> hide #!8 models
> select subtract #12
20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 4 models selected
> select subtract #13
2 models selected
> view matrix models
> #14,0.8016,0.53938,0.25789,-190.17,-0.31968,0.022173,0.94727,58.653,0.50522,-0.84177,0.1902,271.8
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.60959,0.74841,0.2613,-190.74,-0.48817,0.09471,0.86759,104.99,0.62457,-0.65644,0.42309,138.99
> view matrix models
> #14,0.70486,0.64145,0.30284,-200.49,-0.40622,0.015028,0.91365,91.122,0.58151,-0.76701,0.27117,214.19
> view matrix models
> #14,0.54437,0.78241,0.30249,-192.19,-0.33229,-0.12996,0.93418,101.13,0.77022,-0.60906,0.18924,148.52
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.54437,0.78241,0.30249,-195.72,-0.33229,-0.12996,0.93418,109.69,0.77022,-0.60906,0.18924,136.41
> view matrix models
> #14,0.54437,0.78241,0.30249,-197.76,-0.33229,-0.12996,0.93418,110.08,0.77022,-0.60906,0.18924,142.84
> view matrix models
> #14,0.54437,0.78241,0.30249,-199.71,-0.33229,-0.12996,0.93418,111.7,0.77022,-0.60906,0.18924,136.18
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.63312,0.71043,0.30731,-206.86,-0.34688,-0.094512,0.93313,107.36,0.69197,-0.69739,0.1866,177.95
> view matrix models
> #14,0.71087,0.64088,0.28972,-206.15,-0.33815,-0.049762,0.93977,92.873,0.6167,-0.76603,0.18134,214.95
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.71087,0.64088,0.28972,-203.43,-0.33815,-0.049762,0.93977,86.714,0.6167,-0.76603,0.18134,218.04
> fitmap #16 inMap #8
Fit map P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc in map preF_DS-
Cav1_20A_7mpg_Box208_0-045.mrc using 44648 points
correlation = 0.7033, correlation about mean = 0.2694, overlap = 9030
steps = 44, shift = 0.0593, angle = 0.13 degrees
Position of P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc (#16) relative to
preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates:
Matrix rotation and translation
0.63516113 -0.60490130 0.48027571 106.62440954
0.45135795 0.79528046 0.40472829 -149.96457081
-0.62677455 -0.04029141 0.77815825 168.13836967
Axis -0.27926942 0.69472270 0.66284912
Axis point 288.45373559 0.00000000 10.20493332
Rotation angle (degrees) 52.82151862
Shift along axis -22.51035962
> fitmap #13 inMap #14
Fit molecule 102_RSVA-PreF-trimer.pdb (#13) to map
cryosparc_P141_J36_001_volume_map.mrc (#14) using 20544 atoms
average map value = 1.953, steps = 68
shifted from previous position = 3.94
rotated from previous position = 5.86 degrees
atoms outside contour = 2141, contour level = 1.0438
Position of 102_RSVA-PreF-trimer.pdb (#13) relative to
cryosparc_P141_J36_001_volume_map.mrc (#14) coordinates:
Matrix rotation and translation
0.55030849 0.16967080 0.81754047 11.70550044
-0.19361573 0.97837844 -0.07272286 220.29854429
-0.81220289 -0.11826868 0.57126088 -254.98994277
Axis -0.02726701 0.97568173 -0.21748948
Axis point -177.71371795 0.00000000 -121.07794582
Rotation angle (degrees) 56.63477800
Shift along axis 270.07971981
> select clear
> hide #!14 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> ui mousemode right zoom
> select clear
[Repeated 1 time(s)]Drag select of 178 residues
> select up
2123 atoms, 2148 bonds, 274 residues, 1 model selected
> select up
13683 atoms, 13942 bonds, 1771 residues, 1 model selected
> color sel light gray
> select clear
> show #!14 models
> select clear
> color #14 #ff8ad8ff models
> color #14 #ff9ae4ff models
> color #14 #ffd7f5ff models
> transparency 50
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
> true
> vop resample #14 onGrid #8
Opened cryosparc_P141_J36_001_volume_map.mrc resampled as #15, grid size
208,208,208, pixel 2, shown at step 1, values float32
> close #14
> transparency 50
> volume #15 color #f7d5f280
> save "/Users/szhang3/OneDrive -
> Moderna/RSV/MAbs/102/cryosparc_P141_J36_001_volume_map.mrc" models #15
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/102_RSVA-PreF-
> trimer.pdb" models #13 relModel #15
> save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
> true
——— End of log from Tue Jun 17 10:45:24 2025 ———
opened ChimeraX session
> show #!17 models
> hide #!17 models
> hide #!15 models
> hide #!13 models
> show #!16 models
> show #!17 models
> ui mousemode right "rotate selected models"
> select add #17
13451 atoms, 13769 bonds, 4 pseudobonds, 1751 residues, 3 models selected
> view matrix models
> #17,-0.40062,0.51626,-0.75695,335.76,0.73058,-0.3186,-0.60395,309.45,-0.55296,-0.79497,-0.24953,559.08
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.54804,0.83396,-0.064578,107.3,-0.11531,-0.15179,-0.98166,501.63,-0.82847,-0.53054,0.17935,430.99
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.54804,0.83396,-0.064578,139.28,-0.11531,-0.15179,-0.98166,494.56,-0.82847,-0.53054,0.17935,436.13
> view matrix models
> #17,-0.54804,0.83396,-0.064578,144.52,-0.11531,-0.15179,-0.98166,495.92,-0.82847,-0.53054,0.17935,428.28
> view matrix models
> #17,-0.54804,0.83396,-0.064578,140.24,-0.11531,-0.15179,-0.98166,493.11,-0.82847,-0.53054,0.17935,425.39
> view matrix models
> #17,-0.54804,0.83396,-0.064578,143.97,-0.11531,-0.15179,-0.98166,495.1,-0.82847,-0.53054,0.17935,422.32
> ui tool show "Fit in Map"
> fitmap #17 inMap #16
Fit molecule combination (#17) to map P141_J33_zflip_101_RSVA-
mono_MEDI_Mota.mrc (#16) using 13451 atoms
average map value = 1.686, steps = 96
shifted from previous position = 2.18
rotated from previous position = 11.3 degrees
atoms outside contour = 1214, contour level = 1.1617
Position of combination (#17) relative to P141_J33_zflip_101_RSVA-
mono_MEDI_Mota.mrc (#16) coordinates:
Matrix rotation and translation
-0.05730192 0.79167018 -0.60825553 185.35262834
0.35538881 -0.55317279 -0.75345779 457.02248045
-0.93296048 -0.25934179 -0.24965286 501.51117550
Axis 0.67245318 0.44189801 -0.59374478
Axis point 0.00000000 94.20404151 395.46741439
Rotation angle (degrees) 158.44476131
Shift along axis 28.82864470
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc
Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #14, grid size
208,208,208, pixel 2, shown at level 0.0913, step 1, values float32
> close #16
> close #17
> close #14
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/101/101_RSVA-mono_MEDI_Mota.pdb
Chain information for 101_RSVA-mono_MEDI_Mota.pdb #14
---
Chain | Description
B | No description available
C G | No description available
D J | No description available
H | No description available
L | No description available
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc
Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #16, grid size
208,208,208, pixel 2, shown at level 0.0913, step 1, values float32
> volume #16 level 0.5128
> hide #!16 models
> select #14/F:612@CL
1 atom, 1 residue, 1 model selected
> select add #14/A:601@CL
2 atoms, 2 residues, 1 model selected
> select add #14/I:5@C3
3 atoms, 3 residues, 1 model selected
Drag select of 127 atoms
> select up
129 atoms, 137 bonds, 13 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!14 atoms
> show #!14 cartoons
> show #!15 models
> hide #!15 models
> show #!16 models
> color #16 #a6ca8cff models
> transparency 80
> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/MAbs/101/AF_101_fab/101mab/ranked_0.pdb
Chain information for ranked_0.pdb #17
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select add #17
3452 atoms, 3494 bonds, 225 residues, 1 model selected
> view matrix models #17,1,0,0,-50.437,0,1,0,-69.652,0,0,1,86.791
> ui mousemode right zoom
> hide #!16 models
Drag select of 297 residues
> select clear
Drag select of 308 residues, 1 pseudobonds
> select up
2746 atoms, 2811 bonds, 1 pseudobond, 363 residues, 2 models selected
> select up
3237 atoms, 3321 bonds, 1 pseudobond, 424 residues, 2 models selected
Drag select of 225 residues
> ui tool show Matchmaker
> matchmaker #17 & 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 101_RSVA-mono_MEDI_Mota.pdb, chain D (#14) with ranked_0.pdb, chain
A (#17), sequence alignment score = 394.8
RMSD between 114 pruned atom pairs is 0.714 angstroms; (across all 118 pairs:
1.289)
> select clear
> hide #17 models
> select clear
> show #17 models
> hide #17 models
> show #17 models
> select #14/C:108
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #14/D:113
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #14/C:108
17 atoms, 15 bonds, 2 residues, 1 model selected
> hide #17 models
Drag select of 120 residues
> delete atoms sel
> delete bonds sel
> select clear
> select #14/D:43
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 64 residues, 1 pseudobonds
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> select clear
Drag select of 39 residues, 5 pseudobonds
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
Drag select of 2 residues, 1 pseudobonds
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> hide #14.1 models
> select clear
> show #!16 models
> show #17 models
> fitmap #17 inMap #16
Fit molecule ranked_0.pdb (#17) to map P141_J33_zflip_101_RSVA-
mono_MEDI_Mota.mrc (#16) using 3452 atoms
average map value = 1.994, steps = 60
shifted from previous position = 2.12
rotated from previous position = 12.3 degrees
atoms outside contour = 0, contour level = 0.51284
Position of ranked_0.pdb (#17) relative to P141_J33_zflip_101_RSVA-
mono_MEDI_Mota.mrc (#16) coordinates:
Matrix rotation and translation
-0.20789049 0.96779263 0.14198230 194.92116740
0.88526058 0.24789487 -0.39352490 238.81782755
-0.41604718 0.04388125 -0.90828364 246.10281057
Axis 0.61277199 0.78175589 -0.11562099
Axis point 36.69811989 0.00000000 137.78918834
Rotation angle (degrees) 159.08958826
Shift along axis 277.68482618
> volume #16 level 1.817
> volume #16 level 1.078
> select #16
2 models selected
> hide #!16 models
> select subtract #16
Nothing selected
> select #14/B:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/B:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
73 atoms, 72 bonds, 10 residues, 1 model selected
> select up
3482 atoms, 3540 bonds, 449 residues, 1 model selected
> color sel gray
> select clear
Drag select of 306 residues
> select up
2787 atoms, 2841 bonds, 370 residues, 1 model selected
> select up
3237 atoms, 3313 bonds, 428 residues, 1 model selected
> select up
11590 atoms, 11841 bonds, 1514 residues, 1 model selected
> select down
3237 atoms, 3313 bonds, 428 residues, 1 model selected
> color sel orange red
> color sel red
> select clear
Drag select of 256 residues
> select up
2321 atoms, 2376 bonds, 310 residues, 1 model selected
> select up
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> select up
11590 atoms, 11841 bonds, 1514 residues, 1 model selected
> select down
3237 atoms, 3321 bonds, 424 residues, 1 model selected
> color sel yellow
Drag select of 278 residues
> select up
3852 atoms, 3898 bonds, 338 residues, 2 models selected
> select up
4957 atoms, 5024 bonds, 425 residues, 2 models selected
> color sel forest green
> select clear
> select #14/D:114
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
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