![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Last modified 7 months ago
#17671 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-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 0x00000001f74e0840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.core._mac_util, chimerax.graphics._graphics, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, PIL._webp (total: 63)
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
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"CFBundleVersion" : "2575.40.6"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6668853248,
"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" : 6672986112,
"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" : 6691803136,
"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" : 6670479360,
"size" : 270336,
"uuid" : "1480b446-99f7-3757-9d4e-5ba3014a2726",
"path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
"name" : "libsystem_malloc.dylib"
}
],
"sharedCache" : {
"base" : 6668042240,
"size" : 4865835008,
"uuid" : "d326f1a9-b205-3526-879c-7b2105224601"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=13.0G written=7533K(0%) resident=7533K(0%) swapped_out=0K(0%) unallocated=13.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 560K 26 \nColorSync 640K 32 \nCoreAnimation 1696K 94 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 5280K 38 \nDispatch continuations 96.0M 1 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 12.0G 11050 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 41 \nStack 193.9M 41 \nVM_ALLOCATE 350.6M 430 \nVM_ALLOCATE (reserved) 256.0M 1 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 1120 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 644.6M 193 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1140 \n__TPRO_CONST 272K 2 \ndyld private memory 48K 2 \nmapped file 848.7M 115 \nowned unmapped memory 121.3M 1 \npage table in kernel 7533K 1 \nshared memory 3152K 23 \n=========== ======= ======= \nTOTAL 16.0G 17429 \nTOTAL, minus reserved VM space 15.7G 17429 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "89899d2f53ae54f79a95ce4e2faa9b03fb28a5ca",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
},
{
"rolloutId" : "64b21a7351cbb02ce3442e4e",
"factorPackIds" : {
"REMINDERS_GROCERY" : "6647f0f7b6a75d3dc32993e7"
},
"deploymentId" : 240000042
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias roll_movie cofr showpivot false; movie record; roll y 1 360; wait 420;
> movie encode ~/Desktop/roll_movie.mp4; stop
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/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> alignment-with-VAVC.cxs
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
opened ChimeraX session
> hide #!42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> show #!36 models
> hide #!36 models
> show #!36 models
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
> sure.pdb
Summary of feedback from opening
/Users/hemaozhou/Library/CloudStorage/OneDrive-
个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
sure.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0
Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a
180 0
Chain information for A35R-17H1_local_Final_renumber-sure.pdb #46
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide #46#!36 atoms
> show #46#!36 cartoons
> hide #!36 models
> hide #46 models
> show #46 models
> hide #46 models
> show #46 models
> show #35 models
> hide #46 models
> show #46 models
> hide #46 models
> show #46 models
> hide #46 models
> hide #35 models
> show #34 models
> hide #34 models
> show #35 models
> show #34 models
> hide #35 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #34 models
> show #34 models
> show #35 models
> hide #34 models
> close #46#37-45
> combine #35
> rename #37 HCDR1
> rename #38 HCDR2
> rename #39 HCDR3
> rename #40 LCDR1
> rename #41 LCDR2
> rename #42 LCDR3
> hide #37-42 target m
> hide #35 models
> show #37 models
> select #37/H:45-52
67 atoms, 69 bonds, 8 residues, 1 model selected
> select ~sel & ## selected
2318 atoms, 2374 bonds, 297 residues, 1 model selected
> delete sel
> show #37
> hide #!37 cartoons
> color byhetero
> hide #37 atoms
> show #37 atoms
> style #37 stick
Changed 67 atom styles
> show #38 models
> select #38/H:70-77
58 atoms, 59 bonds, 8 residues, 1 model selected
> select ~sel & ## selected
2327 atoms, 2384 bonds, 297 residues, 1 model selected
> delete sel
> show #38
> hide #!38 cartoons
> color byhetero
> style #37-38 stick
Changed 125 atom styles
> select #39/H:116-123
66 atoms, 66 bonds, 8 residues, 1 model selected
> select ~sel & ## selected
2319 atoms, 2377 bonds, 297 residues, 1 model selected
> delete sel
> show #39
> hide #!39 cartoons
> color byhetero
> style #37-38 stick
Changed 125 atom styles
> show #39 models
> style #37-39 stick
Changed 191 atom styles
> select #40/L:46-51
51 atoms, 51 bonds, 6 residues, 1 model selected
> select ~sel & ## selected
2334 atoms, 2392 bonds, 299 residues, 1 model selected
> delete sel
> show #40
> hide #!40 cartoons
> color byhetero
> select #40/L:46-51
51 atoms, 51 bonds, 6 residues, 1 model selected
> select ~sel & ## selected
Nothing selected
> delete sel
> show #40
> hide #!40 cartoons
> color byhetero
> show #40 models
> hide #39 models
> hide #38 models
> hide #37 models
> style #40 stick
Changed 51 atom styles
> show #41 models
> hide #40 models
> select #41/L:69-71
24 atoms, 23 bonds, 3 residues, 1 model selected
> select ~sel & ## selected
2361 atoms, 2420 bonds, 302 residues, 1 model selected
> delete sel
> show #41
> hide #!41 cartoons
> color byhetero
> style #41 stick
Changed 24 atom styles
> hide #41 models
> show #42 models
> select #42/L:108-116
83 atoms, 86 bonds, 9 residues, 1 model selected
> select ~sel & ## selected
2302 atoms, 2357 bonds, 296 residues, 1 model selected
> delete sel
> show #42
> hide #!42 cartoons
> color byhetero
> style #42 stick
Changed 83 atom styles
> hide #42 models
> show #37 models
> hide #37 models
> show #35 models
> combine #35
> hide #35 models
> select #43/A:118-128
77 atoms, 77 bonds, 11 residues, 1 model selected
> select ~sel & ##selected
2308 atoms, 2366 bonds, 294 residues, 1 model selected
> delete sel
> show #43 atoms
> hide #43 cartoons
> style #43 stick
Changed 77 atom styles
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc
Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #44,
grid size 300,300,300, pixel 1.2, shown at level 0.0147, step 1, values
float32
> volume #44 level 6.911
> volume zone #44 nearAtoms #37 range 2.5
> hide #43 models
> show #37 models
> volume #44 style mesh
> volume #44 level 6.762
> volume #44 level 6.194
> volume #44 level 6.493
> view name HCDR1-map
> save /Users/hemaozhou/Desktop/HCDR1-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> hide #!44 models
> show #!44 models
> show #38 models
> hide #37 models
> volume zone #44 nearAtoms #38 range 2.5
> hide #38 models
> show #38 models
> combine #35
> close #38
> combine #35
> rename #38 HCDR2
> close #45
> select #38/H:69-77
70 atoms, 72 bonds, 9 residues, 1 model selected
> select ~sel & ## selected
2315 atoms, 2371 bonds, 296 residues, 1 model selected
> delete sel
> show #38
> hide #!38 cartoons
> color byhetero
> style #38 stick
Changed 70 atom styles
> volume zone #44 nearAtoms #38 range 2.5
> volume #44 level 6.075
> volume #44 level 6.433
> volume #44 level 6.612
> volume #44 level 6.2
> view name HCDR2-map
> save /Users/hemaozhou/Desktop/HCDR2-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> hide #38 models
> show #39 models
> volume zone #44 nearAtoms #39 range 2.5
> volume #44 level 3.931
> volume #44 level 5.722
> volume #44 level 6.021
> volume #44 level 6.319
> volume #44 level 6.2
> view name HCDR3-map
> save /Users/hemaozhou/Desktop/HCDR3-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> volume zone #44 nearAtoms #40 range 2.5
> show #40 models
> hide #39 models
> volume #44 level 6.1
> save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> view name LCDR1-map
> save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> hide #40 models
> show #41 models
> volume zone #44 nearAtoms #41 range 2.5
> volume #44 level 5.8
> volume #44 level 5.5
> volume #44 level 5.8
> view name LCDR2-map
> save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> close #41
> combine #35
> select #41/L:69-71
24 atoms, 23 bonds, 3 residues, 1 model selected
> select ~sel & ## selected
2361 atoms, 2420 bonds, 302 residues, 1 model selected
> delete sel
> show #41
> hide #!41 cartoons
> color byhetero
> style #41 stick
Changed 24 atom styles
> close #41
> combine #35
> select #41/L:68-72
47 atoms, 47 bonds, 5 residues, 1 model selected
> select ~sel & ## selected
2338 atoms, 2396 bonds, 300 residues, 1 model selected
> delete sel
> show #41
> hide #!41 cartoons
> color byhetero
> style #41 stick
Changed 47 atom styles
> volume zone #44 nearAtoms #41 range 2.5
> volume #44 level 6.039
> volume #44 level 5.8
> save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> view name LCDR2-map
> hide #41 models
> show #42 models
> volume zone #44 nearAtoms #42 range 2.5
> volume #44 level 6.2
> view name LCDR3-map
> save /Users/hemaozhou/Desktop/LCDR3-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Density-
> map.cxs
> hide #42 models
> show #43 models
> volume zone #44 nearAtoms #43 range 2.5
> combine #35
> select #45/A:115-127
101 atoms, 102 bonds, 13 residues, 1 model selected
> hide #43 models
> show #43 models
> hide #45 models
> show #45 models
> hide #43 models
> select #45/A:116-127
93 atoms, 94 bonds, 12 residues, 1 model selected
> select #45/A:116-128
98 atoms, 99 bonds, 13 residues, 1 model selected
> select ~sel & ##selected
2287 atoms, 2344 bonds, 292 residues, 1 model selected
> delete sel
> hide #45 atoms
> show #45 atoms
> style #45 stick
Changed 98 atom styles
> hide #45 cartoons
> volume zone #44 nearAtoms #45 range 2.5
> ui tool show "Side View"
> save /Users/hemaozhou/Desktop/A35R-116-128-map-new.tiff width 2794 height
> 2576 supersample 4 transparentBackground true
> volume #44 level 6.5
> volume #44 level 6.4
> volume #44 level 6.3
> save /Users/hemaozhou/Desktop/A35R-116-128-map-new.tiff width 2794 height
> 2576 supersample 4 transparentBackground true
> close #43
> rename #45 A35R-116-128
> combine #35
> hide #45 models
> select #43/A:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #29 models
> hide #29 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #40 models
> hide #40 models
> show #25 models
> show #!26 models
> show #27 models
> show #28 models
> hide #!44 models
> hide #43 models
> hide #28 models
> show #!24 models
> hide #27 models
> hide #!26 models
> show #!26 models
> show #43 models
> hide #43 models
> show #43 models
> hide #!26 models
> show #!26 models
> hide #25 models
> show #25 models
> hide #!24 models
> show #!24 models
> hide #!26 models
> show #!26 models
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> hide #25 models
> select #43/A:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #43/A:173
17 atoms, 15 bonds, 2 residues, 1 model selected
> hide #43 models
> show #43 models
> hide #!24 models
> hide #!26 models
> select #43/A:169-174
45 atoms, 44 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 45 atom styles
> hide sel cartoons
> select ~sel & ##selected
2340 atoms, 2399 bonds, 299 residues, 1 model selected
> delete sel
> volume zone #44 nearAtoms #43 range 2.5
> show #!44 models
> volume #44 level 4.748
> volume #44 level 4.807
> select #43/A:169@N
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> volume zone #44 nearAtoms #43 range 2.5
> volume #44 level 5.046
> volume #44 level 4.986
> volume #44 level 4.927
> view name
Missing or invalid "name" argument: Expected a text string
> view list
Named views: HCDR1, HCDR1-2, HCDR1-map, HCDR2, HCDR2-map, HCDR3, HCDR3-map,
LCDR, LCDR1-map, LCDR2-map, LCDR3-map, Light-footprint, global-rotate90,
global-view
> view HCDR1-map
> save /Users/hemaozhou/Desktop/A35R-170-174-map-new.tiff width 2794 height
> 2576 supersample 4 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Density-
> map.cxs
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #44,
grid size 300,300,300, pixel 1.2, shown at level 6.2, step 1, values float32
Log from Wed May 14 15:05:00 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> alignment-with-VAVC.cxs
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
Log from Tue May 13 23:18:00 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> align-analysis.cxs
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
Log from Wed Apr 30 15:18:22 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Light-
> footprint.cxs format session
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
Log from Tue Apr 22 15:10:46 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/LCDR.cxs
> format session
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
Log from Tue Apr 22 09:51:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR3.cxs
Opened 17H1_global_J192.mrc as #1, grid size 300,300,300, pixel 1.2, shown at
level 4, step 1, values float32
Log from Mon Apr 21 09:13:57 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> global.cxs format session
Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #1,
grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32
Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #13,
grid size 300,300,300, pixel 1.2, shown at level 6.91, step 1, values float32
Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #14,
grid size 300,300,300, pixel 1.2, shown at level 4.14, step 1, values float32
Log from Thu Apr 17 14:20:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> global.cxs
Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #1,
grid size 300,300,300, pixel 1.2, shown at level 4, step 1, values float32
Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #13,
grid size 300,300,300, pixel 1.2, shown at level 6.91, step 1, values float32
Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #14,
grid size 300,300,300, pixel 1.2, shown at level 4.14, step 1, values float32
Opened cryosparc_P23_J197_003_volume_map_sharp (1).mrc as #15, grid size
300,300,300, pixel 1.2, shown at level 0.287, step 1, values float32
Log from Wed Apr 16 23:10:21 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias roll_movie cofr showpivot false; movie record; roll y 1 360; wait 420;
> movie encode ~/Desktop/roll_movie.mp4; stop
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/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc
Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #1,
grid size 300,300,300, pixel 1.2, shown at level 0.0231, step 1, values
float32
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final.pdb
Chain information for A35R-17H1_global_Final.pdb #2
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> volume #1 level 1.575
> set bgColor white
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> color #2/A rgb (245, 204, 114)
> color #2/H rgb (232, 111, 151)
> color #2/L rgb (182, 219, 227)
> lighting soft
> color #2/l,L rgb (245, 204, 114)
> select #2/A
657 atoms, 674 bonds, 1 pseudobond, 83 residues, 2 models selected
> select #2/A,a
1314 atoms, 1348 bonds, 2 pseudobonds, 166 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel dodger blue
> color sel cornflower blue
> color sel dark cyan
> color sel orchid
> color sel slate blue
> color sel dodger blue
> color sel dark turquoise
> color sel dodger blue
> color sel medium spring green
> color sel dodger blue
> color sel cornflower blue
> color sel dodger blue
> select #2/A,a Dodger Blue
Expected a keyword
> select #2/A,a DodgerBlue
Expected a keyword
> color #2/H,h rgb (232, 111, 151)
> select clear
> select add #2
7760 atoms, 7952 bonds, 4 pseudobonds, 1010 residues, 2 models selected
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 7.2
> volume #1 level 3.541
> select subtract #2
Nothing selected
> color zone #1 near #2 distance 4
> color zone #1 near #2 distance 6
> hide #!1 models
> show #!1 models
> hide #!2 models
> ui mousemode right zoom
> lighting soft
> open 4LQF
4lqf title:
Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at
the resolution of 2.3 Angstroms [more info...]
Chain information for 4lqf #3
---
Chain | Description | UniProt
A | A33R | Q71TT1_9POXV 89-185
H | Murine IgG2b A2C7 Heavy chain Fab domain |
L | Murine IgG2b A2C7 Light chain Fab domain |
Non-standard residues in 4lqf #3
---
ZN — zinc ion
4lqf mmCIF Assemblies
---
1| author_defined_assembly
> mmaker #3 to #2
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 A35R-17H1_global_Final.pdb, chain L (#2) with 4lqf, chain L (#3),
sequence alignment score = 645.2
RMSD between 179 pruned atom pairs is 1.260 angstroms; (across all 211 pairs:
1.611)
> hide #!1 models
> show #!2 models
> mmaker #3/A to #2
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 A35R-17H1_global_Final.pdb, chain A (#2) with 4lqf, chain A (#3),
sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> show #!1 models
> hide #!3 models
> show #!3 models
> sym #3
4lqf mmCIF Assemblies
---
1| author_defined_assembly| 2 copies of chains A,H,L
> hide #!2 models
> hide #!1 models
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> hide #!3 models
> show #!3 models
> hide #3.2 models
> hide #3.1 models
> show #3.1 models
> show #3.2 models
> sym #3
4lqf mmCIF Assemblies
---
1| author_defined_assembly| 2 copies of chains A,H,L
> sym #3 axis y
4lqf mmCIF Assemblies
---
1| author_defined_assembly| 2 copies of chains A,H,L
> sym #3 axis x
4lqf mmCIF Assemblies
---
1| author_defined_assembly| 2 copies of chains A,H,L
> show #!1 models
> hide #!1 models
> show #!1 models
> sym #3,C2
Missing or invalid "structures" argument: only initial part "#3" of atom
specifier valid
> sym #3 assembly
Missing "assembly" keyword's argument
> sym #3 assembly identifer
Assembly "identifer" not found, have 1
> sym #3 assembly identifer copies true
Assembly "identifer" not found, have 1
> open 4lqf maxAssemblies 2
'maxAssemblies' has no suffix
> open 4lqf maxAssemblies
'maxAssemblies' has no suffix
> open /Users/hemaozhou/Downloads/4lqf.pdb1
4lqf.pdb1 title:
Structure of murine IGG2B A2C7-fab In complex with vaccinia antigen A33R At
the resolution of 2.3 angstroms [more info...]
Chain information for 4lqf.pdb1
---
Chain | Description
4.1/A | No description available
4.2/A | No description available
4.1/H | No description available
4.2/H | No description available
4.1/L 4.2/L | No description available
> hide #!3 models
> mmaker #4 to #3
Computing secondary structure
[Repeated 2 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 4lqf, chain L (#3) with 4lqf.pdb1, chain L (#4.1), sequence
alignment score = 1139.3
RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs:
0.000)
Matchmaker 4lqf, chain L (#3) with 4lqf.pdb1, chain L (#4.2), sequence
alignment score = 1139.3
RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs:
0.000)
> hide #3.1 models
> hide #!1 models
> hide #3.2 models
> hide #!4 models
> hide #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> show #!4.1 models
Cell requested for row 6 is out of bounds for table with 9 rows! Resizing
table model.
> undo
[Repeated 9 time(s)]
> show #!1 models
> hide #!4.1 models
> show #!4.1 models
> close #4
> open /Users/hemaozhou/Downloads/4lqf.pdb1
4lqf.pdb1 title:
Structure of murine IGG2B A2C7-fab In complex with vaccinia antigen A33R At
the resolution of 2.3 angstroms [more info...]
Chain information for 4lqf.pdb1
---
Chain | Description
4.1/A | No description available
4.2/A | No description available
4.1/H | No description available
4.2/H | No description available
4.1/L 4.2/L | No description available
> mmaker #4.1 to #3
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 4lqf, chain L (#3) with 4lqf.pdb1, chain L (#4.1), sequence
alignment score = 1139.3
RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs:
0.000)
> mmaker #4.2/A to #2
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 A35R-17H1_global_Final.pdb, chain A (#2) with 4lqf.pdb1, chain A
(#4.2), sequence alignment score = 319.5
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> hide #!3 models
> show #!3 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.1 models
> hide #!4 models
> hide #3.2 models
> hide #3.1 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!4.2 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> open /Users/hemaozhou/Downloads/4lqf.pdb1
4lqf.pdb1 title:
Structure of murine IGG2B A2C7-fab In complex with vaccinia antigen A33R At
the resolution of 2.3 angstroms [more info...]
Chain information for 4lqf.pdb1
---
Chain | Description
5.1/A | No description available
5.2/A | No description available
5.1/H | No description available
5.2/H | No description available
5.1/L 5.2/L | No description available
> show #!4.1 models
> show #!4.2 models
> hide #!5.1 models
> close #5.1
> hide #!5.2 models
> show #!5.2 models
> mmaker #5.2/A to #2/a
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 A35R-17H1_global_Final.pdb, chain a (#2) with 4lqf.pdb1, chain A
(#5.2), sequence alignment score = 319.5
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> hide #!4.2 models
> close #4.2
> show #!1 models
> view #1 clip false
> hide #!2 models
> hide #!4 models
> hide #!5 models
> color zone #1 near #2 distance 7
> graphics silhouettes true
> view #1 clip false
> view orient
> ui tool show "Volume Viewer"
> volume #1 level 4.004
> save /Users/hemaozhou/Desktop/A35R-17H1-global.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> view name global-view
> roll y 1 90
> roll x 1 90
> roll x -1 90
> save /Users/hemaozhou/Desktop/A35R-17H1-global-rotate90.tiff width 2794
> height 2576 supersample 4 transparentBackground true
> view name global-rotate90
> hide #!1 models
> show #!2 models
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Global-
> structure.pdb
Cell requested for row 5 is out of bounds for table with 9 rows! Resizing
table model.
Cell requested for row 2 is out of bounds for table with 8 rows! Resizing
table model.
Cell requested for row 0 is out of bounds for table with 7 rows! Resizing
table model.
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final.pdb
Chain information for A35R-17H1_local_Final.pdb #6
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide #!2,6 atoms
> show #!2,6 cartoons
Computing secondary structure
> hide #!2 models
> color #6/A,a Dodger Blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #6/A,a
1314 atoms, 1348 bonds, 2 pseudobonds, 166 residues, 2 models selected
> color sel dodger blue
> color #6/l,L rgb (245, 204, 114)
> color #6/H,h rgb (232, 111, 151)
> select clear
> combine #6
> hide #!6 models
Drag select of 282 residues
> select up
2323 atoms, 2377 bonds, 299 residues, 1 model selected
> delete sel
Drag select of 2 residues
> select up
32 atoms, 33 bonds, 3 residues, 1 model selected
> select up
62 atoms, 64 bonds, 6 residues, 1 model selected
> delete sel
> combine #7
> hide #!8 models
> select #7/A:61,62,64,65,68
37 atoms, 34 bonds, 5 residues, 1 model selected
> view sel
> select #7/A:61,62,64,65,68 #7/H:50,52,118,52,69,71
84 atoms, 77 bonds, 10 residues, 1 model selected
> view sel
> show sel atoms
> style sel stick
Changed 84 atom styles
> color sel byhetero
> select #8/A:67,117,114 #8/L:72,68,110
61 atoms, 57 bonds, 6 residues, 1 model selected
> view sel
No displayed objects specified.
> hide #!7 models
> show #!8 models
> view sel
> show sel atoms
> style sel stick
Changed 61 atom styles
> color sel byhetero
> show #!7 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!8 models
> view sel
> combine #6
> hide #!8 models
> select add #8
2385 atoms, 2445 bonds, 1 pseudobond, 305 residues, 2 models selected
> show #!6 models
> hide #!6 models
> select subtract #8
Nothing selected
> interfaces #!9 & ~solvent
7 buried areas: H L 741, h l 741, H A 524, h a 524, A a 440, L A 307, l a 307
> color #9 byhetero
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
Drag select of 74 residues
> show sel atoms
> style sel stick
Changed 588 atom styles
> color sel byhetero
> select clear
> show #!4 models
> hide #!4 models
> show #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> open
> /Users/hemaozhou/Downloads/fold_2025_03_21_15_41_a35r_dimer/fold_2025_03_21_15_41_a35r_dimer_model_0.cif
Chain information for fold_2025_03_21_15_41_a35r_dimer_model_0.cif #10
---
Chain | Description
A B | .
Computing secondary structure
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A
Alignment identifier is 10/A
> hide #!3 models
> hide #10#!9 atoms
> hide #!9 models
> show #!9 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> close #10
> show #!9 atoms
> hide #!9 atoms
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!7 models
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
Populating font family aliases took 126 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> close #7-9
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!6 models
> hide #!2 models
> ui tool show "Renumber Residues"
> renumber #6/A seqStart 99
83 residues renumbered
> renumber #6/a seqStart 99
83 residues renumbered
> renumber #6/a seqStart 99
0 residues renumbered
> ui tool show "Renumber Residues"
> renumber #2/A seqStart 99
83 residues renumbered
> renumber #2/a seqStart 99
83 residues renumbered
> renumber #2/a seqStart 99
0 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> combine #6
> rename #7 A35R-Heavy
> combine #7
> rename #8 A35R-Light
> combine #6
> rename #9 A35R-17H1_local_Final.pdb
> hide #!9 models
> hide #!6 models
> hide #!8 models
Drag select of 215 residues, 1 pseudobonds
> select up
2021 atoms, 2068 bonds, 1 pseudobond, 257 residues, 2 models selected
> select up
2385 atoms, 2445 bonds, 1 pseudobond, 305 residues, 2 models selected
> delete sel
> select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71
84 atoms, 77 bonds, 10 residues, 1 model selected
Drag select of 26 residues
> select ~sel & ##selected
2186 atoms, 2247 bonds, 1 pseudobond, 279 residues, 2 models selected
> select ~sel & ##selected
199 atoms, 198 bonds, 26 residues, 1 model selected
> select up
272 atoms, 272 bonds, 36 residues, 1 model selected
> select up
837 atoms, 857 bonds, 107 residues, 1 model selected
> delete sel
> select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71
84 atoms, 77 bonds, 10 residues, 1 model selected
> view sel
> show sel atoms
> style sel stick
Changed 84 atom styles
> color sel byhetero
> hide sel atoms
> combine #7
[Repeated 2 time(s)]
> hide #!7 models
> select add #7
1548 atoms, 1588 bonds, 1 pseudobond, 198 residues, 2 models selected
> select subtract #7
Nothing selected
> rename #10 "copy of A35R-Heavy CDR1"
> rename #11 "copy of A35R-Heavy CDR2"
> rename #12 "copy of A35R-Heavy CDR3"
> hide #!12 models
> hide #!11 models
> rename #11 "copy of A35R-Heavy CDR2-3"
> select #10/A:118, 121 #10/H:50,51,52
42 atoms, 40 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 42 atom styles
> color sel byhetero
Drag select of 27 atoms, 57 residues, 23 bonds
> show sel atoms
> style sel stick
Changed 465 atom styles
> show #!1 models
> combine #1
No structures specified
> hide #!1 models
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc
Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #13,
grid size 300,300,300, pixel 1.2, shown at level 0.0147, step 1, values
float32
> volume #13 level 7.728
> volume #13 style mesh
> volume #13 level 6.965
> volume #13 level 5.909
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc
Opened 17H1_global_J192_005_volume_map_Masked_Decon_emready_final.mrc as #14,
grid size 300,300,300, pixel 1.2, shown at level 0.0231, step 1, values
float32
> volume #14 level 6.746
> volume #14 style mesh
> volume #14 level 5.01
> open "/Users/hemaozhou/Downloads/cryosparc_P23_J197_003_volume_map_sharp
> (1).mrc"
Opened cryosparc_P23_J197_003_volume_map_sharp (1).mrc as #15, grid size
300,300,300, pixel 1.2, shown at level 0.0238, step 1, values float32
> volume #15 level 0.5002
> volume #15 level 0.4362
> volume #15 level 0.3793
> volume #14 level 3.245
> volume #14 style surface
> volume #14 level 4.141
> transparency #13 20
> volume #13 style surface
> volume #13 level 4.099
> volume #15 level 0.2869
> volume #13 level 6.905
> hide sel atoms
> select #10/A:118, 121 #10/H:50,51,52
42 atoms, 40 bonds, 5 residues, 1 model selected
> show sel atoms
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #10 to IUPAC-IUB
standards.
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> global.cxs
——— End of log from Wed Apr 16 23:10:21 2025 ———
opened ChimeraX session
> select clear
Cell requested for row 9 is out of bounds for table with 18 rows! Resizing
table model.
> close #10
> combine #11
> hide #!13 models
> clipper off
> mousemode leftMode select control
> mousemode leftMode none control shift
> mousemode middleMode none control
> mousemode wheelMode zoom
> mousemode rightMode none shift
> mousemode wheelMode none control
> mousemode wheelMode none alt
> mousemode wheelMode none shift
> cofr frontCenter showPivot false
> camera mono
> clip off
> lighting soft
> select #10/A:118, 121 #10/H:50,51,52
42 atoms, 40 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 42 atom styles
> color sel byhetero
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> global.cxs
> hide #!10 models
> select add #10
1548 atoms, 1588 bonds, 1 pseudobond, 198 residues, 2 models selected
> select subtract #10
Nothing selected
> show #!1 models
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/09.KP.3.1.1/Deposited_structure/KP311_S_global_J668_007_volume_map_Masked_Decon_emready_inte.mrc
Opened KP311_S_global_J668_007_volume_map_Masked_Decon_emready_inte.mrc as
#16, grid size 400,400,400, pixel 0.76, shown at level 1.33, step 1, values
float32
> hide #!1 models
> view #16 clip false
> color #16 darkgrey models
> color #16 silver models
> save /Users/hemaozhou/Desktop/KP311-trimer.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> close #16
> show #!15 models
> hide #!15 models
> show #!15 models
> close #15
> show #!14 models
> hide #!14 models
> show #!10 models
> view list
Named views: global-rotate90, global-view
> view global-view
> view #10 clip false
> show #!11 models
> hide #!11 models
> select #10/A:118, 121 #10/H:50,51,52
42 atoms, 40 bonds, 5 residues, 1 model selected
> ui mousemode right zoom
> select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71
84 atoms, 77 bonds, 10 residues, 1 model selected
> hide #!10 models
> show #!7 models
> show sel atoms
> style sel stick
Changed 84 atom styles
> select clear
> view list
Named views: global-rotate90, global-view
> view global-view
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Render/Select by Attribute"
> select #7/A:118, 120,121,124,117 #7/H:50,52,118,52,69,71
84 atoms, 77 bonds, 10 residues, 1 model selected
> ui tool show "Basic Actions"
> ui tool show Toolbar
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> cartoon style helix width 1.5 thickness 0.5
> cartoon style strand xsection rectangle width 1.5
> hide sel cartoons
> show sel cartoons
> combine #7
> hide sel cartoons
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #7.1 models
> show #7.1 models
> show #!15 models
> cartoon style strand xsection rectangle width 1.5
[Repeated 1 time(s)]
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> cartoon style strand xsection rectangle width 1.5
> cartoon style helix width 1.5 thickness 0.5
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> transparency #7,15 50 target 50
Invalid "target" argument: Character '5' is not an allowed target, must be one
of acrsbmpfl
> transparency #7,15 50 target c
> hide #!15 models
> show #!15 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select #7/H:70-77
58 atoms, 59 bonds, 8 residues, 1 model selected
> cartoon style width 1.5 thickness 0.5 sel
Expected a keyword
> cartoon style sel width 1.5 thickness 0.5
> cartoon style sel width 3 thickness 0.5
> undo
[Repeated 1 time(s)]
> cartoon style #7/H:70-77 width 3 thickness 0.5
> ribbon style #7/H:70-77 width 3 thick 0.5
> hide #!15 models
> ribbon style #7/H:70-77 width 3 thick 0.5
> ribbon style #7/H:70-77 width 1 thick 0.5
> ribbon tether #7/H:70-77 width 1 thick 0.5
> cartoon tether #7/H:70-77 width 1 thick 0.5
Expected a keyword
> ribbon tether #7/H:70-77 shape cone
> ribbon tether #7/H:70-77 shape steeple
> ribbon tether #7/H:70-77 shape cylinder
> ribbon tether #7/H:70-77 scale 2
> cartoon tether #7/H:70-77 scale 2
Invalid "scale" argument: Must be less than or equal to 1.0
> ribbon tether #7/H:70-77 scale 1
> ribbon tether #7/H:70-77 scale 0.1
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> global.cxs
——— End of log from Thu Apr 17 14:20:34 2025 ———
opened ChimeraX session
> close #13-14
> rename #1 17H1_global_J192.mrc
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!7 models
> select add #7
1548 atoms, 1588 bonds, 1 pseudobond, 198 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!8 models
> show #!10 models
> cartoon style coil thickness 0.25
> select #10/H:42-53
95 atoms, 97 bonds, 12 residues, 1 model selected
> cartoon style coil thickness 0.25 sel
Expected a keyword
> cartoon style sel coil thickness 0.25
Expected a keyword
> cartoon style coil sel thickness 0.25
Expected a keyword
> cartoon style coil #10/H:42-53 l thickness 0.25
Expected a keyword
> cartoon style coil #10/H:42-53 thickness 0.25
Expected a keyword
> cartoon style coil thickness 0.5
> combine #10
> rename #13 "A35R-Heavy CDR2-3"
> hide #!10 models
> show #!10 models
> select #13/H:42-53
95 atoms, 97 bonds, 12 residues, 1 model selected
> select #13/H:43-53
86 atoms, 88 bonds, 11 residues, 1 model selected
> select #13/H:43-52
78 atoms, 80 bonds, 10 residues, 1 model selected
> select ~sel & ##selected
1470 atoms, 1508 bonds, 1 pseudobond, 188 residues, 2 models selected
> delete sel
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!13 atoms
> show #!10 models
> hide #!10 models
> cartoon style coil thickness 1
> show #!10 models
[Repeated 1 time(s)]
> cartoon style coil thickness 0.5 #13
Expected a keyword
> cartoon style #13 thickness 0.5
> cartoon style #13 thickness 1
> cartoon style #13 thickness 0.8
> combine #10
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select #14/H:41-54
113 atoms, 116 bonds, 14 residues, 1 model selected
> select ~sel & ##selected
1435 atoms, 1472 bonds, 1 pseudobond, 184 residues, 2 models selected
> delete sel
> hide #!13 models
> cartoon style #14 thickness 0.8
> cartoon style strand xsection rectangle width 1.5
> hide #!14 models
> close #13-14
> combine #10
> cartoon style helix width 1.5 thickness 0.5
> cartoon style strand xsection rectangle width 1.5
> hide #!13 models
> show #!13 models
> cartoon style #13 thickness 0.8
> hide #!10 models
> show #!10 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> cartoon style (#13 & coil) thickness 0.8
> show #!13 models
> hide #!13 models
> show #!13 models
> cartoon style (#13 & coil) thickness 0.1
> cartoon style (#13 & coil) thickness 0.8
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> cartoon style (#13 & coil) thickness 0.1
> cartoon style (#13 & coil) thickness 0.9
> hide #!13 models
> show #!13 models
> hide #!13 models
> close #13
> combine #10
> cartoon style (#13 & coil) thickness 0.9
> hide #!13 models
> show #!13 models
> cartoon style strand xsection rectangle width 1.5
> cartoon style (#13 & coil) thickness 0.6
> cartoon style (#13 & coil) thickness 0.1
> cartoon style (#13 & coil) thickness 0.2
> cartoon style (#13 & coil) thickness 0.1
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> cartoon style helix width 1.5 thickness 0.5
> show #!13 models
> hide #!13 models
> show #!13 models
> cartoon style strand xsection rectangle width 1.5
> hide #!13 models
> show #!13 models
> cartoon style (#13/H:42-53 & coil) thickness 0.1
> cartoon style (#13/H:42-53 & coil) thickness 0.9
> cartoon style (#13/H:42-53 & coil) thickness 0.5
> cartoon style (#13/H:42-53) thickness 0.5
[Repeated 1 time(s)]
> cartoon style (#13/H:42-53) thickness 0.9
> cartoon style (#13/H:42-53 & coil) thickness 0.5
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #13/H:35-61
212 atoms, 218 bonds, 27 residues, 1 model selected
> select ~sel & ##selected
1336 atoms, 1370 bonds, 1 pseudobond, 171 residues, 2 models selected
> delete sel
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> cartoon style (#13/H:42-53 & coil) thickness 0.5
> show #!13 models
> hide #!13 models
> show #!13 models
> cartoon style (#13/H:42-53 & coil) thickness 0.9
> color #13 magenta
> hide #!13 models
> show #!13 models
> hide #!13 models
> undo
[Repeated 3 time(s)]
> ui tool show "Side View"
> select #13/H:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #13/H:52
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #10/A:118
26 atoms, 25 bonds, 3 residues, 2 models selected
> view sel
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
> graphics silhouettes true
> graphics silhouettes false
> select #13/H:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel target a
> hide #!13 models
> show #!13 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!13 models
> show #!13 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!13 models
> select #10/H:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select clear
> hide #!13 models
> hide #!10 models
> show #!13 models
> hide #!13 atoms
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> select #13/H:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/H:52
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel cartoons
> undo
> hide #!13 models
> select clear
> select #10/H:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #10/H:52
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show #!13 models
> hide #!13 models
> show #!13 models
> select #10/A:118
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select clear
> combine #10/A
> cartoon style helix width 1.5 thickness 0.5
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!10 models
> hide #!14 atoms
> show #!14 cartoons
> delete #14/H
> show #!13 models
> show #!10 models
> transparency 50 target s
> transparency 50 target c
> transparency 10 target c
> transparency 20 target c
> graphics silhouettes true
> view name HCDR1
> ui tool show Distances
> select #10/H:52@N
1 atom, 1 residue, 1 model selected
> select add #10/A:121@OD2
2 atoms, 2 residues, 1 model selected
> distance #10/H:52@N #10/A:121@OD2
Distance between copy of copy of A35R-Heavy CDR2-3 #10/H ASN 52 N and /A ASP
121 OD2: 2.815Å
> distance style symbol false
[Repeated 2 time(s)]
> distance #10/H:52@N #10/A:121@OD2
Distance already exists; modify distance properties with 'distance style'
> hide #16.1 models
> view list
Named views: HCDR1, global-rotate90, global-view
> view HCDR1
> select clear
> hide #!14 models
> select #10/A:118@N
1 atom, 1 residue, 1 model selected
> select add #10/H:50@O
2 atoms, 2 residues, 1 model selected
> distance #10/A:118@N #10/H:50@O
Distance between copy of copy of A35R-Heavy CDR2-3 #10/A SER 118 N and /H ASN
50 O: 3.846
> show #!14 models
> select clear
> view HCDR1
> save /Users/hemaozhou/Desktop/HCDR1.tiff width 2794 height 2576 supersample
> 4 transparentBackground false
> view name HCDR1
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.5
> graphics silhouettes true depthJump 0.6
> graphics silhouettes true depthJump 0.3
> graphics silhouettes true depthJump 0
> graphics silhouettes true depthJump
Missing "depthJump" keyword's argument
> graphics silhouettes true depthJump 0.1
> graphics selection color black
> graphics selection color black width 3
> select #13/H:42-53
95 atoms, 97 bonds, 12 residues, 1 model selected
> select #13/H:42-52
87 atoms, 89 bonds, 11 residues, 1 model selected
> graphics selection color black width 5
> graphics selection color rgb (232, 111, 151) width 4
> graphics selection color rgb (232, 111, 151) width 6
> select #13/H:42-52
87 atoms, 89 bonds, 11 residues, 1 model selected
> graphics selection color rgb (232, 111, 151) width 10
> select #13/H:42-53
95 atoms, 97 bonds, 12 residues, 1 model selected
> graphics silhouettes true depthJump 0.5
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.1
> save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> graphics silhouettes false
> save /Users/hemaozhou/Desktop/HCDR1-3.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> graphics silhouettes true
> hide #!16 models
> rename #16 CDR1
Cell requested for row 15 is out of bounds for table with 17 rows! Resizing
table model.
> show #!16 models
> rename #16 HCDR1
> rename #10 "copy of copy of A35R-Heavy CDR1"
> rename #13 "copy of copy of copy of A35R-Heavy CDR1"
> rename #14 "copy of copy of copy of A35R-Heavy CDR1"
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR1.cxs
> hide #!10 models
> hide #!13 models
> hide #!14 models
> hide #!16 models
> select add #13
212 atoms, 218 bonds, 27 residues, 1 model selected
> show #!11 models
> show #!12 models
> select subtract #13
Nothing selected
> ui tool show "Side View"
> hide #!12 models
> rename #11 "copy of A35R-Heavy CDR2"
> combine #11
> rename #17 "A35R-Heavy CDR2"
> combine #17
> rename #18 "A35R-Heavy CDR2"
> combine #17
> rename #19 "Heavy CDR2"
> 1\. cartoon style helix width 1.5 thick 0.5
Unknown command: 1. cartoon style helix width 1.5 thick 0.5
> cartoon style helix width 1.5 thickness 0.5
> cartoon style strand xsection rectangle width 1.5
> hide #!19 models
> hide #!18 models
> select #17/H:69,71 #17/A:117,124
34 atoms, 31 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> show #!18 models
> select #11/A:124
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> select #17/A:124
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show #!18 models
> select clear
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> ui tool show Distances
> select #17/A:124@O
1 atom, 1 residue, 1 model selected
> select add #17/H:69@OH
2 atoms, 2 residues, 1 model selected
> distance #17/A:124@O #17/H:69@OH
Distance between A35R-Heavy CDR2 #17/A ALA 124 O and /H TYR 69 OH: 3.365
> select #17/H:71@OD1
1 atom, 1 residue, 1 model selected
> select add #17/A:117@NZ
2 atoms, 2 residues, 1 model selected
> distance #17/H:71@OD1 #17/A:117@NZ
Distance between A35R-Heavy CDR2 #17/H ASP 71 OD1 and /A LYS 117 NZ: 2.995
> distance style color #00f900
[Repeated 2 time(s)]
> undo
[Repeated 1 time(s)]
> distance style color #fffb00
[Repeated 2 time(s)]
> undo
[Repeated 2 time(s)]
> select clear
> color sel green
> select clear
> hide #20.1 models
> select #17/H:69,71 #17/A:117,124
34 atoms, 31 bonds, 2 pseudobonds, 4 residues, 2 models selected
> view sel
> select clear
> view name HCDR2
> show #!19 models
> hide #!18 models
> hide #!17 models
> select #19/H:65-85
173 atoms, 179 bonds, 21 residues, 1 model selected
> select ~sel & ##selected
1375 atoms, 1409 bonds, 1 pseudobond, 177 residues, 2 models selected
> delete sel
> hide #!19 models
> show #!19 models
> hide #!11 models
> cartoon style (#19/H:42-53 & coil) thickness 0.9
> cartoon style (#19/H:70-77 & coil) thickness 0.9
[Repeated 1 time(s)]
> show #!18 models
> show #!17 models
> transparency 50 target c
> transparency 20 target c
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> save /Users/hemaozhou/Desktop/HCDR2.tiff width 2794 height 2576 supersample
> 4 transparentBackground false
> rename #20 HCDR2
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!16 models
> show #!15 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!14 models
> show #!10 models
> hide #!15 models
> select #13/H:42-52
87 atoms, 89 bonds, 11 residues, 1 model selected
> show #!17 models
> show #!18 models
> show #!19 models
> show #!20 models
> show #20.1 models
> hide #20.1 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> graphics selection color red width 10
> select clear
> graphics selection color rgb (232, 111, 190) width 10
> select #13/H:42-52
87 atoms, 89 bonds, 11 residues, 1 model selected
> color violet #13/H:42-52
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #13/H:42-52
87 atoms, 89 bonds, 11 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> select clear
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select #19/H:70-77
58 atoms, 59 bonds, 8 residues, 1 model selected
> color sel violet
> undo
> select #19/H:71-76
43 atoms, 44 bonds, 6 residues, 1 model selected
> color sel violet
> select clear
> hide #!18 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select #19/H:79
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #19/H:80
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #19/H:81
29 atoms, 27 bonds, 3 residues, 1 model selected
> select add #10/H:82
38 atoms, 35 bonds, 4 residues, 2 models selected
> hide sel cartoons
> select add #19/H:82
47 atoms, 43 bonds, 5 residues, 2 models selected
> hide sel cartoons
> select add #17/H:82
56 atoms, 51 bonds, 6 residues, 3 models selected
> hide sel cartoons
> hide #!17 models
> show #!17 models
> select clear
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select #19/H:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> undo
[Repeated 1 time(s)]
> select #19/H:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> hide sel atoms
> hide #!19 models
> show #!19 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select #19/H:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> hide #!17 models
> show #!17 models
> hide #!19 models
> show #!19 models
> hide sel atoms
> select clear
> hide #!17 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> view name HCDR1-2
> save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR1-2.cxs
> select #10/H:118
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #10/A:120
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> undo
Cell requested for row 19 is out of bounds for table with 21 rows! Resizing
table model.
> hide #!20 models
> hide #!19 models
> hide #!17 models
> hide #!16 models
> hide #!14 models
> hide #!13 models
> hide #!10 models
> show #!11 models
> select add #10
1548 atoms, 1588 bonds, 3 pseudobonds, 198 residues, 3 models selected
> select subtract #10
Nothing selected
> hide #!11 models
> show #!12 models
> combine #12
> rename #21 "A35R-Heavy CDR3"
> rename #12 "A35R-Heavy CDR3"
> combine #21
[Repeated 1 time(s)]
> rename #22 "A35R-Heavy CDR3"
> rename #23 "A35R-Heavy CDR3"
> cartoon style helix width 1.5 thickness 0.5
> cartoon style strand xsection rectangle width 1.5
> hide #!23 models
> hide #!22 models
> select add #12/H:118
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #12/A:120
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show #!22 models
> select clear
> select #23/H:110-130
167 atoms, 171 bonds, 21 residues, 1 model selected
> show #!23 models
> select ~sel & ##selected
1381 atoms, 1417 bonds, 1 pseudobond, 177 residues, 2 models selected
> delete sel
> hide #!22 models
> show #!22 models
> hide #!21 models
> show #!21 models
> cartoon style (#23 & coil) thickness 0.9
> hide #!21 models
> hide #!22 models
> hide #!12 models
Drag select of 16 residues
> select subtract #23/H:117
118 atoms, 15 residues, 1 model selected
> hide sel cartoons
> show #!22 models
> show #!21 models
> hide #!22 models
> hide #!21 models
> select add #23/H:117
129 atoms, 10 bonds, 16 residues, 1 model selected
> hide sel cartoons
> show #!22 models
> show #!21 models
> hide #!21 models
> hide #!22 models
> show #!22 models
> show #!21 models
> select #21/H:118 #21/A:120
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> view list
Named views: HCDR1, HCDR1-2, HCDR2, global-rotate90, global-view
> view HCDR1-2
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> select clear
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.01
> graphics silhouettes true depthJump 0.1
> select #23/H:118-122
38 atoms, 37 bonds, 5 residues, 1 model selected
> color sel violet
> select clear
> ui tool show Distances
> select #21/H:118@NH2
1 atom, 1 residue, 1 model selected
> select add #21/A:120@OE2
2 atoms, 2 residues, 1 model selected
> distance #21/H:118@NH2 #21/A:120@OE2
Distance between A35R-Heavy CDR3 #21/H ARG 118 NH2 and /A GLU 120 OE2: 2.985
> select #21/H:118@NH2
1 atom, 1 residue, 1 model selected
> select add #21/A:120@OE1
2 atoms, 2 residues, 1 model selected
> distance #21/H:118@NH2 #21/A:120@OE1
Distance between A35R-Heavy CDR3 #21/H ARG 118 NH2 and /A GLU 120 OE1: 2.859
> select #21/H:118@NE
1 atom, 1 residue, 1 model selected
> select add #21/A:120@OE1
2 atoms, 2 residues, 1 model selected
> distance #21/H:118@NE #21/A:120@OE1
Distance between A35R-Heavy CDR3 #21/H ARG 118 NE and /A GLU 120 OE1: 3.581
> distance style color #8efa00
[Repeated 2 time(s)]
> distance style color #00f900
[Repeated 2 time(s)]
> hide #24.1 models
> select clear
> view list
Named views: HCDR1, HCDR1-2, HCDR2, global-rotate90, global-view
> view HCDR1-2
> ui tool show "Side View"
> view HCDR1-2
> hide #!23 models
> show #!23 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!23 models
> show #!22 models
> hide #!21 models
> show #!21 models
> hide #!24 models
> show #!24 models
> show #!23 models
> select #23/H:118
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #22/A:120
20 atoms, 18 bonds, 2 residues, 2 models selected
> view sel
> select clear
> graphics silhouettes false
> graphics silhouettes true
> select #23/H:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #23/H:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #23/H:117
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel violet
> select clear
> view name HCDR3
> save /Users/hemaozhou/Desktop/HCDR3.tiff width 2794 height 2576 supersample
> 4 transparentBackground false
> hide #!24 models
> hide #!23 models
> hide #!22 models
> hide #!21 models
> color #20 #00f900ff models
> show #!20 models
> show #20.1 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!10 models
> show #!13 models
> show #!14 models
> show #!16 models
> hide #!18 models
> view list
Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, global-rotate90, global-view
> view HCDR1-2
> hide #20.1 models
> color #20.1 #fffb00ff models
> show #20.1 models
> hide #20.1 models
> show #20.1 models
> hide #20.1 models
> color lemonchiffon sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel lomon
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lemonchiffon
> select clear
> color sel yellow
> select clear
> color sel orange
> select clear
> color sel yellow
[Repeated 1 time(s)]
> select clear
> save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> select clear
> save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/HCDR3.cxs
——— End of log from Mon Apr 21 09:13:57 2025 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> ui mousemode right zoom
Cell requested for row 17 is out of bounds for table with 26 rows! Resizing
table model.
> hide #!17 models
> hide #!19 models
> hide #!20 models
Cell requested for row 15 is out of bounds for table with 25 rows! Resizing
table model.
> hide #!16 models
> hide #!14 models
> hide #!13 models
> hide #!10 models
> show #!9 models
> show #!7 models
> hide #!9 models
> show #!8 models
> hide #!7 models
> combine #8
[Repeated 3 time(s)]
> cartoon style helix width 1.5 thickness 0.5
> cartoon style strand xsection rectangle width 1.5
> hide #!28 models
> hide #!27 models
> hide #!26 models
> select #25/L: 68,72,110 #25/A:123,170,167
52 atoms, 49 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 52 atom styles
> color sel byhetero
> hide #!8 models
> delete #25/H
> show #!26 models
> hide #!26 models
> delete #26/H
> select #26/L:60-76
132 atoms, 133 bonds, 17 residues, 1 model selected
> show #!26 models
> select #26/L:60-78
146 atoms, 148 bonds, 19 residues, 1 model selected
> select #26/L:60-80
163 atoms, 165 bonds, 21 residues, 1 model selected
> select #26/L:60-80, 106-120
287 atoms, 294 bonds, 36 residues, 1 model selected
> select ~sel & ##selected
3592 atoms, 3682 bonds, 2 pseudobonds, 459 residues, 2 models selected
> delete sel
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> delete sel
> cartoon style (#26 & coil) thickness 0.9
> hide #!25 models
> select #26/L:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #26/L:65
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #26/L:64
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #26/L:63
31 atoms, 28 bonds, 4 residues, 1 model selected
> select add #26/L:76
35 atoms, 31 bonds, 5 residues, 1 model selected
> select add #26/L:77
42 atoms, 37 bonds, 6 residues, 1 model selected
> select add #26/L:79
48 atoms, 42 bonds, 7 residues, 1 model selected
> select add #26/L:78
55 atoms, 49 bonds, 8 residues, 1 model selected
> select add #26/L:80
66 atoms, 59 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select add #26/L:106
78 atoms, 71 bonds, 10 residues, 1 model selected
> select add #26/L:107
84 atoms, 76 bonds, 11 residues, 1 model selected
> select add #26/L:108
92 atoms, 83 bonds, 12 residues, 1 model selected
> select add #26/L:119
96 atoms, 86 bonds, 13 residues, 1 model selected
> select add #26/L:118
100 atoms, 89 bonds, 14 residues, 1 model selected
> select add #26/L:117
111 atoms, 100 bonds, 15 residues, 1 model selected
> select add #26/L:116
118 atoms, 106 bonds, 16 residues, 1 model selected
> select add #26/L:120
122 atoms, 109 bonds, 17 residues, 1 model selected
> select add #26/L:62
128 atoms, 114 bonds, 18 residues, 1 model selected
> select add #26/L:61
137 atoms, 122 bonds, 19 residues, 1 model selected
> select add #26/L:60
141 atoms, 125 bonds, 20 residues, 1 model selected
> hide sel cartoons
> show #!25 models
> trasn 50 target r
Unknown command: trasn 50 target r
> transparency 50 target r
> select #25/L:110
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> transparency 20 target r
> select #25/A:170@OD2
1 atom, 1 residue, 1 model selected
> select add #25/L:72@NE
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #25/A:170@OD2 #25/L:72@NE
Distance between copy of A35R-Light #25/A ASP 170 OD2 and /L ARG 72 NE: 2.916
> show #!24 models
> distance style color #00f900
[Repeated 2 time(s)]
> select #25/L:72@NH1
1 atom, 1 residue, 1 model selected
> select add #25/A:170@OD2
2 atoms, 2 residues, 1 model selected
> distance #25/L:72@NH1 #25/A:170@OD2
Distance between copy of A35R-Light #25/L ARG 72 NH1 and /A ASP 170 OD2: 4.493
> show #24.1 models
> hide #24.1 models
> show #24.1 models
> distance style color #8efa00
[Repeated 2 time(s)]
> distance style color #00f900
[Repeated 2 time(s)]
> hide #24.1 models
> show #24.1 models
> hide #24.1 models
> delete sel
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> select add #24
5 pseudobonds, 2 models selected
> hide #!24 models
> select #25/L:72@NE
1 atom, 1 residue, 1 model selected
> select add #25/A:170@OD2
2 atoms, 2 residues, 1 model selected
> distance #25/L:72@NE #25/A:170@OD2
Distance already exists; modify distance properties with 'distance style'
> show #!24 models
> close #24
> select #25/L:72@NE
1 atom, 1 residue, 1 model selected
> select add #25/A:170@OD2
2 atoms, 2 residues, 1 model selected
> distance #25/L:72@NE #25/A:170@OD2
Distance between copy of A35R-Light #25/L ARG 72 NE and /A ASP 170 OD2: 2.916
> select #25/L:72@NH2
1 atom, 1 residue, 1 model selected
> select add #25/A:170@OD2
2 atoms, 2 residues, 1 model selected
> distance #25/L:72@NH2 #25/A:170@OD2
Distance between copy of A35R-Light #25/L ARG 72 NH2 and /A ASP 170 OD2: 3.112
> hide #24.1 models
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber.pdb
Chain information for A35R-17H1_local_Final_renumber.pdb #29
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide #!25 models
> hide #!26 models
> select add #25
3879 atoms, 3976 bonds, 4 pseudobonds, 495 residues, 3 models selected
> select subtract #25
Nothing selected
> style #29 stick
Changed 4770 atom styles
> hide #29 atoms
> show #29 cartoons
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #29 models
> show #29 models
Drag select of 268 residues
> select up
2265 atoms, 2318 bonds, 292 residues, 1 model selected
> select up
2385 atoms, 2446 bonds, 305 residues, 1 model selected
> delete sel
> hide #29 models
> show #29 models
> show #!26 models
> hide #!26 models
> show #!26 models
> show #!27 models
> hide #!27 models
> show #!25 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> close #25
> close #27-28
> rename #29 A35R-17H1_local_Light.pdb
> combine #29
> hide #!26 models
> show #!26 models
> show #29 models
> hide #29 models
> hide #!26 models
> show #!26 models
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> hide #24 models
> select subtract #24
Nothing selected
> rename #25 A35R-17H1_local_Light.pdb
> combine #29
[Repeated 1 time(s)]
> rename #27 A35R-17H1_local_Light.pdb
> rename #28 A35R-17H1_local_Light.pdb
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> cartoon style helix width 1.5 thickness 0.5
> cartoon style strand xsection rectangle width 1.5
> show #29 models
> color #25,27-29/l,L rgb (245, 204, 114)
> color #25,27-29/A,a Dodger Blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #25,27-29/A
2628 atoms, 2700 bonds, 332 residues, 4 models selected
> ui tool show "Color Actions"
> color sel dodger blue
> select clear
> hide #28 models
> hide #29 models
> hide #27 models
> hide #25 models
> show #25 models
> delete #25/H
> view list
Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, global-rotate90, global-view
> view HCDR3
> select #25/L: 68,72,110 #25/A:123,170,167
61 atoms, 57 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 61 atom styles
> color sel byhetero
> show #!26 models
> select clear
> transparency 20 target r
> show #24 models
> hide #24 models
> show #24 models
> ui tool show Distances
> select #26/L:110
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide #!26 models
> select #25/L:110
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show #!26 models
> select clear
> select #25/A:167@OD2
1 atom, 1 residue, 1 model selected
> select add #25/L:72@NE
2 atoms, 2 residues, 1 model selected
> distance #25/A:167@OD2 #25/L:72@NE
Distance between A35R-17H1_local_Light.pdb #25/A ASP 167 OD2 and /L ARG 72 NE:
2.916
> select #25/L:72@NH2
1 atom, 1 residue, 1 model selected
> select add #25/A:167@OD2
2 atoms, 2 residues, 1 model selected
> distance #25/L:72@NH2 #25/A:167@OD2
Distance between A35R-17H1_local_Light.pdb #25/L ARG 72 NH2 and /A ASP 167
OD2: 3.112
> select #25/L:68@OH
1 atom, 1 residue, 1 model selected
> select add #25/A:170@NE2
2 atoms, 2 residues, 1 model selected
> distance #25/L:68@OH #25/A:170@NE2
Distance between A35R-17H1_local_Light.pdb #25/L TYR 68 OH and /A GLN 170 NE2:
3.318
> select add #25/A:123@NZ
3 atoms, 3 residues, 1 model selected
> select add #25/L:110@O
4 atoms, 4 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #25/L:110@O
1 atom, 1 residue, 1 model selected
> select add #25/A:123@NZ
2 atoms, 2 residues, 1 model selected
> distance #25/L:110@O #25/A:123@NZ
Distance between A35R-17H1_local_Light.pdb #25/L TYR 110 O and /A LYS 123 NZ:
3.206
> select clear
> hide #24.1 models
> distance style color #fffb00
[Repeated 2 time(s)]
> undo
[Repeated 3 time(s)]
> hide #24.1 models
> distance style color #00f900
[Repeated 2 time(s)]
> color sel orange
> color sel yellow
> color sel orange
> select clear
> graphics silhouettes false
> graphics silhouettes width 2
> graphics silhouettes true
> graphics silhouettes width 3
> graphics silhouettes width 2
> save /Users/hemaozhou/Desktop/LCDR.tiff width 2794 height 2576 supersample 4
> transparentBackground false
[Repeated 1 time(s)]
> view name LCDR
> hide #25 models
> show #25 models
> hide #!26 models
> show #!26 models
> color #26 #ff7e79ff
> color #26 #ffd479ff
> color #26 #ff9300ff
> transparency 20 target r
> select clear
> color sel cyan
> select clear
> save /Users/hemaozhou/Desktop/LCDR.tiff width 2794 height 2576 supersample 4
> transparentBackground false
> hide #!24 models
> hide #25 models
> hide #!26 models
> show #!10 models
> show #!13 models
> show #!14 models
> show #!16 models
> show #!17 models
> show #!19 models
> show #!20 models
> viee list
Unknown command: viee list
> viee listview list
Unknown command: viee listview list
> view list
Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, LCDR, global-rotate90, global-view
> view HCDR1-2
[Repeated 1 time(s)]
> transparency 20 target r
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!20 models
> show #!20 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!14 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> transparency 20 target r,c
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> transparency 20 target c
> color sel cyan
> select clear
> save /Users/hemaozhou/Desktop/HCDR1-2.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/LCDR.cxs
——— End of log from Tue Apr 22 09:51:42 2025 ———
opened ChimeraX session
> open 1HZH
Summary of feedback from opening 1HZH fetched from pdb
---
notes | Fetching compressed mmCIF 1hzh from http://files.rcsb.org/download/1hzh.cif
Fetching CCD FUC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/FUC/FUC.cif
Fetching CCD GAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GAL/GAL.cif
1hzh title:
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]
Chain information for 1hzh #30
---
Chain | Description | UniProt
H K | IMMUNOGLOBULIN HEAVY CHAIN | IGG1_HUMAN 111-478
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein | Q8TCD0_HUMAN 107-214
Non-standard residues in 1hzh #30
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> mmaker 20 to #19
> matchmaker 20 to #19
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker #20 to #19
No molecules/chains to match specified
> mmaker #20 to #17
No molecules/chains to match specified
> mmaker #30 to #17
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 A35R-Heavy CDR2, chain H (#17) with 1hzh, chain K (#30), sequence
alignment score = 345.1
RMSD between 112 pruned atom pairs is 0.851 angstroms; (across all 115 pairs:
1.054)
> show #25 models
> hide #25 models
> show #25 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!2 models
> mmaker #30 to #2
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 A35R-17H1_global_Final.pdb, chain H (#2) with 1hzh, chain H (#30),
sequence alignment score = 737.4
RMSD between 188 pruned atom pairs is 1.145 angstroms; (across all 211 pairs:
1.712)
> hide #!2 models
> hide #!30 models
> hide #25 models
> show #25 models
> hide #25 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #29 models
> combine #29
> hide #29 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #!10 models
> hide #!13 models
> hide #!14 models
> hide #!16 models
> hide #!17 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
Drag select of 116 residues
> select up
1311 atoms, 1339 bonds, 164 residues, 1 model selected
> select up
1728 atoms, 1771 bonds, 222 residues, 1 model selected
> delete sel
> surface #32
No atoms specified by #32
> surface #31
> transparency 0 target s
> show #29 models
> select #31/A:119-120,123-124,127-128,154,167,169-170
73 atoms, 68 bonds, 10 residues, 1 model selected
> hide #29 models
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for copy of A35R-17H1_local_Light.pdb_A SES surface #31.1:
minimum, -16.74, mean -3.85, maximum 7.71
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> coulombic #31
Coulombic values for copy of A35R-17H1_local_Light.pdb_A SES surface #31.1:
minimum, -16.74, mean -3.85, maximum 7.71
> transparency 20 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 20 target s sel
Expected a keyword
> transparency sel 20 target s
> show #29 models
> hide #29 models
> show #25 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #29 models
> transparency sel 50 target s
> hide #31.1 models
> show #31.1 models
> hide #29 models
> transparency sel 100 target s
> transparency sel 0 target s
> combine #32
No structures specified
> combine #31
> hide #31.1 models
> show #31.1 models
> coulombic #31 offset
Missing "offset" keyword's argument
> ~coulombic #31
Unknown command: ~coulombic #31
> hide #31.1 models
> show #31.1 models
> surface #31
> hide #31.1 models
> close #31.1
> surface #31
> transparency 0 target s
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #31.1 models
> show #31.1 models
> hide #31.1 models
> hide #!31 models
> surface #32
> hide #!32 models
> show #!2 models
> surface #2
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #!2 models
> show #!31 models
> show #31.1 models
> hide #31.1 models
> select clear
> style #!31 stick
Changed 657 atom styles
> select clear
> style #!31 stick
Changed 657 atom styles
> select clear
Drag select of 83 residues
> style sel stick
Changed 657 atom styles
> show sel atoms
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
> sure.pdb
Summary of feedback from opening
/Users/hemaozhou/Library/CloudStorage/OneDrive-
个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
sure.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0
Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a
180 0
Chain information for A35R-17H1_local_Final_renumber-sure.pdb #33
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide sel atoms
> select clear
> hide #33#!31 atoms
> show #33#!31 atoms
> hide #33#!31 atoms
> show #33#!31 cartoons
> hide #!31 models
> hide #33 models
> show #33 models
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final-
> renumber-sure_副本.pdb
Chain information for A35R-17H1_global_Final-renumber-sure_副本.pdb #34
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> show #33#!34 cartoons
Computing secondary structure
> hide #33#!34 atoms
> hide #33 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #!34 models
> show #!34 models
> show #33 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #33 models
> hide #!32 models
> show #!32 models
> show #33 models
> hide #!32 models
> close #33#34
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
> sure.pdb
Summary of feedback from opening
/Users/hemaozhou/Library/CloudStorage/OneDrive-
个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
sure.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0
Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a
180 0
Chain information for A35R-17H1_local_Final_renumber-sure.pdb #33
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide #33 atoms
> show #33 cartoons
> surface #33/A
> hide #!33 cartoons
> select #33/A
657 atoms, 674 bonds, 83 residues, 1 model selected
> color sel dodger blue
> select clear
> combine #33
> show #!32 models
> select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118,
> 120-121,123-125,128,172-173,175,178
196 atoms, 186 bonds, 25 residues, 2 models selected
> hide #!32 models
> show #!32 models
> hide #!33 models
> show #!33 models
> hide #!32 models
> select add #32
776 atoms, 789 bonds, 98 residues, 4 models selected
> select subtract #32
119 atoms, 114 bonds, 15 residues, 3 models selected
> show #!32 models
> select add #32
776 atoms, 789 bonds, 98 residues, 3 models selected
> select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118,
> 120-121,123-125,128,172-173,175,178
196 atoms, 186 bonds, 25 residues, 2 models selected
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> trasns 0
Unknown command: trasns 0
> transparency 0
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> show #29 models
> hide #!32 models
> hide #!33 models
> hide #34 models
> show #34 models
> show #!33 models
> select add #34
4966 atoms, 5072 bonds, 635 residues, 5 models selected
> hide #!33 models
> select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118,
> 120-121,123-125,128,172-173,175,178
196 atoms, 186 bonds, 25 residues, 2 models selected
> hide #34 models
> show #!33 models
> show #!32 models
> hide #!33 models
> hide #!32 models
> show #!32 models
> show sel & #!32 atoms
> hide #!32 models
> select #29/A:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
50 atoms, 52 bonds, 5 residues, 1 model selected
> select up
657 atoms, 675 bonds, 83 residues, 1 model selected
> show sel atoms
> select #32/A:119-120,123-124,127-128,154,170,172-173 #33/A:114-118,
> 120-121,123-125,128,172-173,175,178
196 atoms, 186 bonds, 25 residues, 2 models selected
> show #!32 models
> hide #!32 models
> show #!32 models
> select add #33
4847 atoms, 4958 bonds, 620 residues, 4 models selected
> select subtract #33
77 atoms, 72 bonds, 10 residues, 3 models selected
> hide #29 models
> hide #!32 models
> show #!32 models
> show #29 models
> select #32/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> combine #29
> hide #29 models
> hide #!32 models
> hide #35 models
> show #35 models
Drag select of 127 atoms, 107 bonds, 32 residues
> select up
272 atoms, 269 bonds, 38 residues, 1 model selected
> select up
310 atoms, 313 bonds, 38 residues, 1 model selected
> select up
519 atoms, 532 bonds, 65 residues, 1 model selected
> select up
657 atoms, 675 bonds, 83 residues, 1 model selected
> delete sel
> select #35/H:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
59 atoms, 61 bonds, 6 residues, 1 model selected
> select up
891 atoms, 914 bonds, 115 residues, 1 model selected
> delete sel
> show #!32 models
> select #32/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> show #29 models
> hide #29 models
> show sel atoms
> hide #!32 models
> show #!32 models
> combine #32
> select #36/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> show sel atoms
> select #32/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> transparency sel 20 target s
> transparency sel 40 target s
> select #36/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> show sel cartoons
> hide #35 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> transparency 0 target r
> show #!32 models
> color sel byhetero
> select clear
> select #36/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> select #32/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> show #35 models
> hide #35 models
> show #35 models
> hide #36 models
> show #36 models
> show #28 models
> hide #28 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> select #35/L:109-116, 66-74
153 atoms, 156 bonds, 17 residues, 1 model selected
> select #35/L:109-116, 66-74,45-52
218 atoms, 221 bonds, 25 residues, 1 model selected
> combine #35
> hide #37 models
> select ~sel & ##selected
619 atoms, 636 bonds, 82 residues, 1 model selected
> delete sel
> select #32/A:164@C
1 atom, 1 residue, 1 model selected
> delete sel
> hide sel
> cartoon style (#35 & coil) thickness 0.9
> cartoon style (#35 & coil) thickness 1.5
> cartoon style (#35 & coil) thickness 1
> hide #36 models
> show #36 models
> hide #36 models
> hide #!32 models
> show #!32 models
> show #36 models
> hide #36 models
> show #36 models
> hide #!35 models
> show #!35 models
> select #32/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> transparency sel 50 target s
> select clear
> select #32/A:119-120,123-124,127-128,154,170,172-173
77 atoms, 72 bonds, 10 residues, 1 model selected
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> show #37 models
> select #37/L:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #35/L:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #34 models
> hide #34 models
> hide #37 models
> show #34 models
> hide #!32 models
> hide #!35 models
> hide #36 models
> hide #34 models
> show #34 models
> show #34 cartoons
> show #36 models
> hide #36 models
> close #36-37#35
> undo
> show #!33 models
> show #!32 models
> hide #!33 models
> hide #34 models
> hide #!32 models
> show #!32 models
> close #32
Cell requested for row 39 is out of bounds for table with 43 rows! Resizing
table model.
> close #31
> show #!33 models
> select #33/A:119-120,123-124,127-128,154,170,172-173
73 atoms, 68 bonds, 10 residues, 1 model selected
> show #25 models
> show #34 models
> hide #!33 models
Drag select of 262 residues
> select up
2266 atoms, 2318 bonds, 291 residues, 1 model selected
> select up
2385 atoms, 2443 bonds, 305 residues, 1 model selected
> delete sel
> hide #25 models
> color #34/l,L rgb (245, 204, 114)
> color #34/H,h rgb (232, 111, 151)
> show #!33 models
> hide #!33 models
> hide #34 models
> show #34 models
> combine #34
[Repeated 2 time(s)]
> rename #34 A35R-17H1_local_Final_renumber-sure.pdb
> rename #35 A35R-17H1_local_Final_renumber-sure.pdb
> rename #31 A35R-17H1_local_Final_renumber-sure.pdb
> rename #32 A35R-17H1_local_Final_renumber-sure.pdb
> show #!33 models
> hide #32 models
> hide #31 models
> hide #34 models
> hide #35 models
> show #35 models
> hide #35 models
> select #33/A:119-120,123-124,127-128,154,170,172-173
73 atoms, 68 bonds, 10 residues, 1 model selected
> show #31 models
> hide #!33 models
> show #!33 models
> hide #31 models
> show #31 models
> hide #!33 models
Drag select of 96 residues
> select up
1245 atoms, 1272 bonds, 159 residues, 1 model selected
> select up
1728 atoms, 1769 bonds, 222 residues, 1 model selected
> delete sel
> show #!33 models
> select #33/A:119-120,123-124,127-128,154,170,172-173
73 atoms, 68 bonds, 10 residues, 1 model selected
> transparency sel 50 target s
> show sel atoms
> style sel stick
Changed 73 atom styles
> color (#!33 & sel) byhetero
> color #33 target s
> color #33 blue target s
> transparency sel 50 target s
> color sel dodger blue
> color (#!33 & sel) byhetero
> color #33 dodger blue target s
> transparency sel 50 target s
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> select #31/A:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #31/A:169
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show #32 models
> rename #32 A35R-17H1_local_Final_renumber-sure-lightchain.pdb
> hide #!33 models
> hide #31 models
Drag select of 4 residues
Drag select of 2 residues
> select up
68 atoms, 66 bonds, 10 residues, 1 model selected
> select up
1548 atoms, 1587 bonds, 198 residues, 1 model selected
> delete sel
> show #!33 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #32 models
> hide #!33 models
> show #!33 models
> hide #31 models
> show #31 models
> hide #!33 models
> show #!33 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #32 models
> select #32/L:109-116, 66-74,45-52
218 atoms, 221 bonds, 25 residues, 1 model selected
> select ~sel & ##selected
619 atoms, 635 bonds, 82 residues, 1 model selected
> delete sel
> hide sel
> cartoon style (#32 & coil) thickness 1
> hide #!33 models
> show #!33 models
> select #33/A:119-120,123-124,127-128,154,170,172-173
73 atoms, 68 bonds, 10 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide #!32 models
> show #!32 models
> hide #!33 models
> show #!33 models
> select clear
> show #!32-33 cartoons
> hide #!32 models
> hide #!33 models
> show #!33 models
Drag select of 110 residues
Drag select of 86 residues
> select up
2503 atoms, 2558 bonds, 317 residues, 1 model selected
> select up
4113 atoms, 4212 bonds, 527 residues, 1 model selected
> delete sel
> show #!32 models
> hide #!33 models
> show #!33 models
> transparency 0 target r
> select #33/A:119-120,123-124,127-128,154,170,172-173
73 atoms, 68 bonds, 10 residues, 1 model selected
> transparency sel 80 target s
> graphics silhouettes false
> graphics silhouettes true
> transparency sel 60 target s
> transparency #32 50 target r
> transparency #32 20 target r
> graphics selection color rgb (245, 204, 114) width 10
> view name Light-footprint
> save /Users/hemaozhou/Desktop/Light-footprint.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> graphics selection color rgb (245, 204, 114) width 20
> graphics selection color rgb (245, 204, 114) width 30
> graphics selection color rgb (245, 204, 114) width 20
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> save /Users/hemaozhou/Desktop/Light-footprint-2.tiff width 2794 height 2576
> supersample 4 transparentBackground false
> graphics selection color rgb (245, 204, 114) width 30
> save /Users/hemaozhou/Desktop/Light-footprint-3.tiff width 2794 height 2576
> supersample 4 transparentBackground false
[Repeated 1 time(s)]
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Light-
> footprint.cxs
——— End of log from Tue Apr 22 15:10:46 2025 ———
opened ChimeraX session
> select add #33
657 atoms, 674 bonds, 83 residues, 3 models selected
> hide #!33 models
> hide #!32 models
> show #!30 models
> hide #!30 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> show #34 models
> show #35 models
> hide #35 models
> hide #34 models
> select subtract #33
1 model selected
> show #34 models
> view #34 clip false
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final-
> renumber-sure.pdb
Summary of feedback from opening
/Users/hemaozhou/Library/CloudStorage/OneDrive-
个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final-
renumber-sure.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0
Start residue of secondary structure not found: SHEET 37 3737 THR a 178 HIS a
180 0
Chain information for A35R-17H1_global_Final-renumber-sure.pdb #36
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide #34#!36 atoms
> show #34#!36 cartoons
> hide #34 models
> select #236A,a Dodger Blue
Expected an objects specifier or a keyword
> select #36A,a Dodger Blue
Expected an objects specifier or a keyword
> ui tool show "Color Actions"
> select #36/A,a
1314 atoms, 1348 bonds, 166 residues, 1 model selected
> color sel dodger blue
> color #36/l,L rgb (245, 204, 114)
> color #36/H,h rgb (232, 111, 151)
> select clear
Drag select of 299 residues
> select up
2937 atoms, 2996 bonds, 382 residues, 1 model selected
> select up
3880 atoms, 3972 bonds, 505 residues, 1 model selected
> delete sel
> open 4LQF
4lqf title:
Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at
the resolution of 2.3 Angstroms [more info...]
Chain information for 4lqf #37
---
Chain | Description | UniProt
A | A33R | Q71TT1_9POXV 89-185
H | Murine IgG2b A2C7 Heavy chain Fab domain |
L | Murine IgG2b A2C7 Light chain Fab domain |
Non-standard residues in 4lqf #37
---
ZN — zinc ion
4lqf mmCIF Assemblies
---
1| author_defined_assembly
> hide #!36 models
> view #37 clip false
> open 4LU5
Summary of feedback from opening 4LU5 fetched from pdb
---
note | Fetching compressed mmCIF 4lu5 from http://files.rcsb.org/download/4lu5.cif
4lu5 title:
Structure of murine IgG2a A20G2-Fab in complex with vaccinia antigen A33R at
the resolution of 2.9 Angstroms [more info...]
Chain information for 4lu5 #38
---
Chain | Description | UniProt
A B | A33R | Q71TT1_9POXV 89-185
H I | Murine IgG2a A20G2 Heavy chain Fab domain |
L M | Murine IgG2a A20G2 Light chain Fab domain |
> undo
[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.
> close #36
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final-
> renumber-sure.pdb
Summary of feedback from opening
/Users/hemaozhou/Library/CloudStorage/OneDrive-
个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_global_Final-
renumber-sure.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0
Start residue of secondary structure not found: SHEET 37 3737 THR a 178 HIS a
180 0
Chain information for A35R-17H1_global_Final-renumber-sure.pdb #36
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> show #!36-38 cartoons
> hide #!36-38 atoms
> select #36/A,a
1314 atoms, 1348 bonds, 166 residues, 1 model selected
> open 4LQF
4lqf title:
Structure of murine IgG2b A2C7-Fab in complex with vaccinia antigen A33R at
the resolution of 2.3 Angstroms [more info...]
Chain information for 4lqf #39
---
Chain | Description | UniProt
A | A33R | Q71TT1_9POXV 89-185
H | Murine IgG2b A2C7 Heavy chain Fab domain |
L | Murine IgG2b A2C7 Light chain Fab domain |
Non-standard residues in 4lqf #39
---
ZN — zinc ion
4lqf mmCIF Assemblies
---
1| author_defined_assembly
> color #36/H,h rgb (232, 111, 151)
> color #36/l,L rgb (245, 204, 114)
> select #36/A,a
1314 atoms, 1348 bonds, 166 residues, 1 model selected
> color sel dodger blue
> close #39
> select add #36
7760 atoms, 7944 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> select subtract #36
Nothing selected
> mmaker #37 to #36
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 A35R-17H1_global_Final-renumber-sure.pdb, chain L (#36) with 4lqf,
chain L (#37), sequence alignment score = 645.2
RMSD between 179 pruned atom pairs is 1.260 angstroms; (across all 211 pairs:
1.611)
> mmaker #38 to #36
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 A35R-17H1_global_Final-renumber-sure.pdb, chain L (#36) with 4lu5,
chain M (#38), sequence alignment score = 677.2
RMSD between 69 pruned atom pairs is 0.980 angstroms; (across all 211 pairs:
6.470)
> view #36 clip false
> mmaker #38 to #36/A
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 A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lu5,
chain A (#38), sequence alignment score = 332.4
RMSD between 77 pruned atom pairs is 0.667 angstroms; (across all 83 pairs:
1.746)
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!37 models
> mmaker #37 to #36/A
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 A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf,
chain A (#37), sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> open 4M1G
Summary of feedback from opening 4M1G fetched from pdb
---
note | Fetching compressed mmCIF 4m1g from http://files.rcsb.org/download/4m1g.cif
4m1g title:
Structure of murine IgG2a A27D7-Fab in complex with vaccinia antigen A33R at
the resolution of 1.6 Angstroms [more info...]
Chain information for 4m1g #39
---
Chain | Description | UniProt
A B | A33R | Q71TT1_9POXV 89-185
H | Murine IgG2a A27D7 Heavy chain Fab domain |
L | Murine IgG2a A27D7 Light chain Fab domain |
Non-standard residues in 4m1g #39
---
SO4 — sulfate ion
> mmaker #39 to #36/A
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 A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4m1g,
chain A (#39), sequence alignment score = 346.8
RMSD between 71 pruned atom pairs is 0.786 angstroms; (across all 82 pairs:
1.630)
> hide #!38 models
> show #!38 models
> hide #!36-39 atoms
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 58572 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> undo
> hide #!37 models
> show #!37 models
> sym #37
4lqf mmCIF Assemblies
---
1| author_defined_assembly| 2 copies of chains A,H,L
> sym #37 assembly 1
Made 2 copies for 4lqf assembly 1
> view
> mmaker #40 to #36/A
Computing secondary structure
[Repeated 2 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 A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf,
chain A (#40.1), sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
Matchmaker A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf,
chain A (#40.2), sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> undo
> mmaker #40.1 to #36/A
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 A35R-17H1_global_Final-renumber-sure.pdb, chain A (#36) with 4lqf,
chain A (#40.1), sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> mmaker #40.2 to #36/a
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 A35R-17H1_global_Final-renumber-sure.pdb, chain a (#36) with 4lqf,
chain A (#40.2), sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
> close #40
> sym #37
4lqf mmCIF Assemblies
---
1| author_defined_assembly| 2 copies of chains A,H,L
> show #!37 models
> sym #37 assembly 1
Made 2 copies for 4lqf assembly 1
> view
> merge #40.1 #40.2
Unknown command: merge #40.1 #40.2
> combine #40.1 #40.2
Remapping chain ID 'A' in 4lqf #40.2 to 'B'
Remapping chain ID 'H' in 4lqf #40.2 to 'I'
Remapping chain ID 'L' in 4lqf #40.2 to 'M'
> hide #!40.1 models
> hide #!40 models
> hide #!40.2 models
> hide #!41 models
> show #!41 models
> mmaker #41 to #36/a
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 A35R-17H1_global_Final-renumber-sure.pdb, chain a (#36) with
combination, chain A (#41), sequence alignment score = 339
RMSD between 76 pruned atom pairs is 0.695 angstroms; (across all 78 pairs:
0.850)
Cell requested for row 36 is out of bounds for table with 43 rows! Resizing
table model.
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> align-analysis.cxs
——— End of log from Wed Apr 30 15:18:22 2025 ———
opened ChimeraX session
> show #!40 models
> hide #!40 models
> hide #!38 models
> show #!38 models
> hide #!39 models
> show #!39 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!39 models
> show #!39 models
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/4LU5.pdb
> models #38 relModel #36
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/4M1G.pdb
> models #39 relModel #36
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/4LQF.pdb
> models #41 relModel #36
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/A35R-17H1.pdb
> models #36 relModel #36
> ui tool show "Color Actions"
> hide #!36 models
> show #!36 models
> combine #38
> combine #39
> combine #41
> rename #44 "copy of 4lqf"
> combine #36
> hide #!36 models
> hide #!38 models
> hide #!39 models
> hide #!44 models
> hide #!41 models
> hide #!43 models
> hide #!42 models
> show #!44 models
> hide #!45 models
Drag select of 60 residues
> select up
829 atoms, 850 bonds, 105 residues, 1 model selected
> select up
1222 atoms, 1252 bonds, 156 residues, 1 model selected
> delete sel
> show #!43 models
> hide #!44 models
Drag select of 50 residues
> select up
801 atoms, 819 bonds, 100 residues, 1 model selected
> select up
1276 atoms, 1306 bonds, 163 residues, 1 model selected
> delete sel
> show #!42 models
> hide #!43 models
Drag select of 45 residues
> select up
703 atoms, 719 bonds, 87 residues, 1 model selected
> select up
1350 atoms, 1380 bonds, 173 residues, 1 model selected
> delete sel
> hide #!42 models
> show #!42 models
> show #!43 models
> color #42 #73fdffff
> color #43 #d783ffff
> show #!44 models
> color #44 #ff7e79ff
> show #!45 models
> surface #42-44
> lighting soft
> surface #45/H,h,L,l
> transparency #42-45 50
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 5
> graphics silhouettes width 3
> graphics silhouettes width 2
> graphics silhouettes #42 width 2
Expected true or false or a keyword
> graphics silhouettes #42 width 5
Expected true or false or a keyword
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> graphics silhouettes width 5
> graphics silhouettes width 3
> graphics silhouettes width 2
> hide #!45 models
> show #!45 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> transparency #42-45 10
> lighting flat
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting flat
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.4
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.2
> lighting soft
> graphics silhouettes true depthJump 0.3
> graphics silhouettes width 4
> graphics silhouettes width 2
> graphics silhouettes width 3
> graphics silhouettes width 2
> select add #42
6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 2 models selected
> select subtract #42
4 models selected
> select add #42
6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 2 models selected
> select subtract #42
4 models selected
> select add #42
6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 2 models selected
> select add #43
10397 atoms, 10100 bonds, 3 pseudobonds, 1831 residues, 8 models selected
> select add #44
17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 13 models selected
> select add #45
24915 atoms, 24804 bonds, 27 pseudobonds, 3873 residues, 19 models selected
> select subtract #45
17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 21 models selected
> select subtract #44
10397 atoms, 10100 bonds, 3 pseudobonds, 1831 residues, 14 models selected
> select subtract #43
6658 atoms, 6764 bonds, 2 pseudobonds, 916 residues, 8 models selected
> select subtract #42
4 models selected
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes true depthJump 0.2
> transparency #42-45 50
> transparency #42-45 0
> transparency #42-45 10
> transparency #42-45 20
> hide #!45 models
> show #!45 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> select add #43
3739 atoms, 3336 bonds, 1 pseudobond, 915 residues, 2 models selected
> select subtract #43
2 models selected
> select add #43
3739 atoms, 3336 bonds, 1 pseudobond, 915 residues, 2 models selected
> graphics silhouettes true depthJump 0.6
> graphics silhouettes true depthJump 0.2
> select subtract #43
2 models selected
> select add #43
3739 atoms, 3336 bonds, 1 pseudobond, 915 residues, 2 models selected
> select subtract #43
2 models selected
> hide #!44 models
> hide #!42 models
> graphics silhouettes false
> graphics silhouettes true
> show #!44 models
> show #!42 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> graphics silhouettes true depthJump 0.1
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!44 models
> show #!44 models
> hide #!43 models
> show #!43 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> color #42 #ff2f92ff
> color #42 #ff7e79ff
> color #42 #ffd479ff
> color #42 #fffc79ff
> color #42 #d4fb79ff
> color #42 #fffc79ff
> color #42 #d4fb79ff
> color #42 #73fa79ff
> hide #!43 models
> show #!43 models
> transparency #42-45 0
> hide #!44 models
> hide #!43 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> show #!42 models
> show #!43 models
> show #!44 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> graphics selection color black width 3
> select add #44
6758 atoms, 6760 bonds, 22 pseudobonds, 1032 residues, 3 models selected
> select subtract #44
4 models selected
> select add #44
6758 atoms, 6760 bonds, 22 pseudobonds, 1032 residues, 3 models selected
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.3
> graphics silhouettes true depthJump 0.5
> graphics silhouettes true depthJump 0.8
> graphics silhouettes true depthJump 0.2
> select subtract #44
4 models selected
> hide #!44 models
> hide #!43 models
> hide #!42 models
> transparency #45 80
> show #!44 models
> transparency #44-45 80
> show #!43 models
> show #!42 models
> transparency #42-45 80
> graphics silhouettes false
> select add #44
6758 atoms, 6760 bonds, 22 pseudobonds, 1032 residues, 3 models selected
> select add #43
10497 atoms, 10096 bonds, 23 pseudobonds, 1947 residues, 9 models selected
> select add #42
17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 13 models selected
> select add #45
24915 atoms, 24804 bonds, 27 pseudobonds, 3873 residues, 19 models selected
> select subtract #45
17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 21 models selected
> select #42-44, #45/H,h,L,l
Expected an objects specifier or a keyword
> select #42-44, sel #45/H,h,L,l
Expected an objects specifier or a keyword
> select #42-44 sel #45/H,h,L,l
Expected a keyword
> select #42-44
17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 7 models selected
> select #45/H,h,L,l
6446 atoms, 6596 bonds, 2 pseudobonds, 844 residues, 2 models selected
> select #42-44
17155 atoms, 16860 bonds, 25 pseudobonds, 2863 residues, 7 models selected
> select #42-44, #45/H,h,L,l
Expected an objects specifier or a keyword
> select #42-44, 45/H,h,L,l
16733 atoms, 16693 bonds, 15 pseudobonds, 2573 residues, 9 models selected
> select #42-44, 45/H,h,L,l,M
20181 atoms, 20172 bonds, 25 pseudobonds, 3061 residues, 9 models selected
> select #42-44, 45/H,h,L,l,M,N
20181 atoms, 20172 bonds, 25 pseudobonds, 3061 residues, 9 models selected
> select #42-44, 45/H,h,L,l,M,N,I
23413 atoms, 23456 bonds, 27 pseudobonds, 3519 residues, 9 models selected
> transparency (#!42-45 & sel) 10
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.4
> graphics silhouettes true depthJump 0.6
> transparency (#!42-45 & sel) 0
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true depthJump 0.2
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> transparency (#!42-45 & sel) 10
> lighting soft
> transparency (#!42-45 & sel) 0
Drag select of copy of 4lu5_L SES surface, 32351 of 197904 triangles, copy of
4lqf_H SES surface, 49873 of 184766 triangles, copy of 4lqf_L SES surface,
100098 of 200140 triangles, copy of A35R-17H1_global_Final-renumber-sure.pdb_h
SES surface, 96576 of 199722 triangles, copy of A35R-17H1_global_Final-
renumber-sure.pdb_l SES surface, 97071 of 206196 triangles, 423 residues, 2
pseudobonds
> select up
3838 atoms, 3912 bonds, 2 pseudobonds, 506 residues, 10 models selected
> select up
8215 atoms, 8415 bonds, 2 pseudobonds, 1072 residues, 10 models selected
> select up
8291 atoms, 8415 bonds, 2 pseudobonds, 1148 residues, 10 models selected
> select ~sel & ##selected
12885 atoms, 13053 bonds, 14 pseudobonds, 1810 residues, 7 models selected
> select clear
> view list
Named views: HCDR1, HCDR1-2, HCDR2, HCDR3, LCDR, Light-footprint, global-
rotate90, global-view
> view global-view
> view Light-footprint
> view global-view
> graphics silhouettes true depthJump 0.2
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> hide #!44 models
> show #!44 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> select clear
> hide sel
> select clear
> hide #43.1 models
> hide #43.2 models
> hide #43.3 models
> show #43.3 models
> show #43.2 models
> save /Users/hemaozhou/Desktop/structural-comparison.tiff width 2794 height
> 2576 supersample 4 transparentBackground true
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Structure-
> alignment-with-VAVC.cxs
——— End of log from Tue May 13 23:18:00 2025 ———
opened ChimeraX session
> hide #!42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> show #!36 models
> hide #!36 models
> show #!36 models
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
> sure.pdb
Summary of feedback from opening
/Users/hemaozhou/Library/CloudStorage/OneDrive-
个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/A35R-17H1_local_Final_renumber-
sure.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 3 THR A 178 HIS A 180 0
Start residue of secondary structure not found: SHEET 23 2323 THR a 178 HIS a
180 0
Chain information for A35R-17H1_local_Final_renumber-sure.pdb #46
---
Chain | Description
A a | No description available
H h | No description available
L l | No description available
> hide #46#!36 atoms
> show #46#!36 cartoons
> hide #!36 models
> hide #46 models
> show #46 models
> hide #46 models
> show #46 models
> show #35 models
> hide #46 models
> show #46 models
> hide #46 models
> show #46 models
> hide #46 models
> hide #35 models
> show #34 models
> hide #34 models
> show #35 models
> show #34 models
> hide #35 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #34 models
> show #34 models
> show #35 models
> hide #34 models
> close #46#37-45
> combine #35
[Repeated 5 time(s)]
> rename #37 HCDR1
> rename #38 HCDR2
> rename #39 HCDR3
> rename #40 LCDR1
> rename #41 LCDR2
> rename #42 LCDR3
> hide #37-42 target m
> hide #35 models
> show #37 models
> select #37/H:45-52
67 atoms, 69 bonds, 8 residues, 1 model selected
> select ~sel & ## selected
2318 atoms, 2374 bonds, 297 residues, 1 model selected
> delete sel
> show #37
> hide #!37 cartoons
> color byhetero
> hide #37 atoms
> show #37 atoms
> style #37 stick
Changed 67 atom styles
> show #38 models
> select #38/H:70-77
58 atoms, 59 bonds, 8 residues, 1 model selected
> select ~sel & ## selected
2327 atoms, 2384 bonds, 297 residues, 1 model selected
> delete sel
> show #38
> hide #!38 cartoons
> color byhetero
> style #37-38 stick
Changed 125 atom styles
> select #39/H:116-123
66 atoms, 66 bonds, 8 residues, 1 model selected
> select ~sel & ## selected
2319 atoms, 2377 bonds, 297 residues, 1 model selected
> delete sel
> show #39
> hide #!39 cartoons
> color byhetero
> style #37-38 stick
Changed 125 atom styles
> show #39 models
> style #37-39 stick
Changed 191 atom styles
> select #40/L:46-51
51 atoms, 51 bonds, 6 residues, 1 model selected
> select ~sel & ## selected
2334 atoms, 2392 bonds, 299 residues, 1 model selected
> delete sel
> show #40
> hide #!40 cartoons
> color byhetero
> select #40/L:46-51
51 atoms, 51 bonds, 6 residues, 1 model selected
> select ~sel & ## selected
Nothing selected
> delete sel
> show #40
> hide #!40 cartoons
> color byhetero
> show #40 models
> hide #39 models
> hide #38 models
> hide #37 models
> style #40 stick
Changed 51 atom styles
> show #41 models
> hide #40 models
> select #41/L:69-71
24 atoms, 23 bonds, 3 residues, 1 model selected
> select ~sel & ## selected
2361 atoms, 2420 bonds, 302 residues, 1 model selected
> delete sel
> show #41
> hide #!41 cartoons
> color byhetero
> style #41 stick
Changed 24 atom styles
> hide #41 models
> show #42 models
> select #42/L:108-116
83 atoms, 86 bonds, 9 residues, 1 model selected
> select ~sel & ## selected
2302 atoms, 2357 bonds, 296 residues, 1 model selected
> delete sel
> show #42
> hide #!42 cartoons
> color byhetero
> style #42 stick
Changed 83 atom styles
> hide #42 models
> show #37 models
> hide #37 models
> show #35 models
> combine #35
> hide #35 models
> select #43/A:118-128
77 atoms, 77 bonds, 11 residues, 1 model selected
> select ~sel & ##selected
2308 atoms, 2366 bonds, 294 residues, 1 model selected
> delete sel
> show #43 atoms
> hide #43 cartoons
> style #43 stick
Changed 77 atom styles
> open /Users/hemaozhou/Library/CloudStorage/OneDrive-
> 个人/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Final_map/17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc
Opened 17H1_local_J197_003_volume_map_Masked_Decon_emready_final.mrc as #44,
grid size 300,300,300, pixel 1.2, shown at level 0.0147, step 1, values
float32
> volume #44 level 6.911
> volume zone #44 nearAtoms #37 range 2.5
> hide #43 models
> show #37 models
> volume #44 style mesh
> volume #44 level 6.762
> volume #44 level 6.194
> volume #44 level 6.493
> view name HCDR1-map
> save /Users/hemaozhou/Desktop/HCDR1-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> hide #!44 models
> show #!44 models
> show #38 models
> hide #37 models
> volume zone #44 nearAtoms #38 range 2.5
> hide #38 models
> show #38 models
> combine #35
> close #38
> combine #35
> rename #38 HCDR2
> close #45
> select #38/H:69-77
70 atoms, 72 bonds, 9 residues, 1 model selected
> select ~sel & ## selected
2315 atoms, 2371 bonds, 296 residues, 1 model selected
> delete sel
> show #38
> hide #!38 cartoons
> color byhetero
> style #38 stick
Changed 70 atom styles
> volume zone #44 nearAtoms #38 range 2.5
> volume #44 level 6.075
> volume #44 level 6.433
> volume #44 level 6.612
> volume #44 level 6.2
> view name HCDR2-map
> save /Users/hemaozhou/Desktop/HCDR2-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> hide #38 models
> show #39 models
> volume zone #44 nearAtoms #39 range 2.5
> volume #44 level 3.931
> volume #44 level 5.722
> volume #44 level 6.021
> volume #44 level 6.319
> volume #44 level 6.2
> view name HCDR3-map
> save /Users/hemaozhou/Desktop/HCDR3-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> volume zone #44 nearAtoms #40 range 2.5
> show #40 models
> hide #39 models
> volume #44 level 6.1
> save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> view name LCDR1-map
> save /Users/hemaozhou/Desktop/LCDR1-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> hide #40 models
> show #41 models
> volume zone #44 nearAtoms #41 range 2.5
> volume #44 level 5.8
> volume #44 level 5.5
> volume #44 level 5.8
> view name LCDR2-map
> save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> close #41
> combine #35
> select #41/L:69-71
24 atoms, 23 bonds, 3 residues, 1 model selected
> select ~sel & ## selected
2361 atoms, 2420 bonds, 302 residues, 1 model selected
> delete sel
> show #41
> hide #!41 cartoons
> color byhetero
> style #41 stick
Changed 24 atom styles
> close #41
> combine #35
> select #41/L:68-72
47 atoms, 47 bonds, 5 residues, 1 model selected
> select ~sel & ## selected
2338 atoms, 2396 bonds, 300 residues, 1 model selected
> delete sel
> show #41
> hide #!41 cartoons
> color byhetero
> style #41 stick
Changed 47 atom styles
> volume zone #44 nearAtoms #41 range 2.5
> volume #44 level 6.039
> volume #44 level 5.8
> save /Users/hemaozhou/Desktop/LCDR2-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> view name LCDR2-map
> hide #41 models
> show #42 models
> volume zone #44 nearAtoms #42 range 2.5
> volume #44 level 6.2
> view name LCDR3-map
> save /Users/hemaozhou/Desktop/LCDR3-map-new.tiff width 2794 height 2576
> supersample 4 transparentBackground true
> save
> /Users/hemaozhou/OneDrive/00.Papers/0.Manuscripts/11.Mpoxv/01.Structure/Structure_figure/Density-
> map.cxs
——— End of log from Wed May 14 15:05:00 2025 ———
opened ChimeraX session
> rename #41 LCDR2
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AV0005NCH/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 11881.81.2
OS Loader Version: 11881.81.2
Software:
System Software Overview:
System Version: macOS 15.3 (24D60)
Kernel Version: Darwin 24.3.0
Time since boot: 35天30分钟
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Redmi 27 NU:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
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-clix: 0.2.0
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: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
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
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
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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