![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18211 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
seLast 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 0x0000000205b39f00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PIL._webp, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 57)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
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"modelCode" : "MacBookAir10,1",
"coalitionID" : 14409,
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-07-16 01:47:13.2732 -0500",
"codeSigningMonitor" : 1,
"incident" : "952B01D6-3419-4B71-BA6D-EA5C8EC16718",
"pid" : 73875,
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"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-12 16:25:34.4052 -0500",
"procStartAbsTime" : 5084681826345,
"procExitAbsTime" : 8988256744608,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"57A90D80-F304-5878-AA3D-33EE15DFFA9E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C26E1A6D-208C-0431-BC9F-D1252B1481C3",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "5E937FEF-F94E-4FDD-A6EE-D7E1BB5B4750",
"wakeTime" : 20373,
"sleepWakeUUID" : "25F8C2A6-F556-4247-9A9C-99F895ECDC62",
"sip" : "enabled",
"vmRegionInfo" : "0x707da866e108 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000707da866e108","rawCodes":[1,123684998537480],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000707da866e108"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":73875},
"vmregioninfo" : "0x707da866e108 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
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"name" : "CoreFoundation",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/Structure/KSHV_Prefusion_gB.pdb"
Chain information for KSHV_Prefusion_gB.pdb #1
---
Chain | Description
A B C | No description available
> select bg white
Expected an objects specifier or a keyword
> set bgColor white
> graphics silhouettes true
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/cyro-EM/cryosparc_P986_J74_007_volume_map_sharp.mrc"
Opened cryosparc_P986_J74_007_volume_map_sharp.mrc as #2, grid size
384,384,384, pixel 0.933, shown at level 0.0154, step 2, values float32
> volume #2 step 1
> surface dust #2 size 9.33
> volume #2 level 0.065
> transparency 50
> select #1:53-78, 511-617
5886 atoms, 5940 bonds, 372 residues, 1 model selected
> color sel #cc9900ff
> select #1:79-92, 456-510
3429 atoms, 3465 bonds, 207 residues, 1 model selected
> color sel #ccff00ff
> select #1:93-104, 312-409
5079 atoms, 5151 bonds, 330 residues, 1 model selected
> color sel #33cc66ff
> select #1:105-311
9696 atoms, 9819 bonds, 621 residues, 1 model selected
> color sel #0099ccff
> select #1:618-690
3465 atoms, 3492 bonds, 219 residues, 1 model selected
> color sel #ff0000ff
> select add #1
28563 atoms, 28935 bonds, 3 pseudobonds, 1785 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
2 models selected
No visible atoms or bonds selected
> hide #!1 models
No visible atoms or bonds selected
> transparency sel 0
No visible atoms or bonds selected
> color #2 white models
> color #2 #d6d6d6ff models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> transparency sel 50
> transparency sel 0
> show #!1 models
> transparency sel 50
> transparency #2.1 100
> hide #!1 models
> show #!1 models
> lighting soft
> cartoon style width 2.5 thickness 0.8
> hide #1 atoms
> ui mousemode right select
> select clear
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> ui tool show "Side View"
> view sel
> view
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> view
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select add #1
28563 atoms, 28935 bonds, 3 pseudobonds, 1785 residues, 2 models selected
> select add #2
28563 atoms, 28935 bonds, 3 pseudobonds, 1785 residues, 6 models selected
> select subtract #1
4 models selected
> select clear
> transparency 80
> select add #2
4 models selected
> select clear
> select add #2
4 models selected
> transparency #2.1 100
> select clear
> select add #2
4 models selected
> select subtract #2
Nothing selected
> view
> lighting soft
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> select add #2
4 models selected
> transparency #2.1 90
> select clear
> select add #2
4 models selected
> graphics silhouettes false
> select clear
> select add #2
4 models selected
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting soft
> transparency #2.1 100
> select clear
> hide H
> select clear
> view
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> view
> select #1/a:311
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> delete H
> cd "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3"
Current working directory is: /Users/kjyeol/Library/CloudStorage/Box-
Box/McLellan Lab/Manuscripts/In Progress/KSHV_gB/Figures/Figure3
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_Pro311_1.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select #1/a:191 #1/c:627
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/a:191 #1/c:627
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/a:191 #1/c:627
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> hide #!2 models
> select #1/a:105#1/c:627
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> select #1/a:105 #1/c:627
10 atoms, 8 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> show #!2 models
> volume #2 level 0.05139
> volume #2 level 0.04166
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 120
> volume #2 level 0.04
Drag select of 2 atoms, 1 bonds, 2 cryosparc_P986_J74_007_volume_map_sharp.mrc
> select #2
4 models selected
> select #2
4 models selected
Drag select of 2 cryosparc_P986_J74_007_volume_map_sharp.mrc
> select clear
> volume #2 level 0.05
> volume #2 level 0.04
> volume #2 level 0.045
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> trun y 120
Unknown command: trun y 120
> turn y 120
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_627.tif"
> width 2400 height 1814 supersample 3
> volume #2 level 0.05
> surface dust #2 size 9.33
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select /A:105
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /C:628
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> ui mousemode right "rotate selected models"
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> show #!2 models
> volume #2 level 0.065
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> size stickRadius 0.3
Changed 14865 bond radii
> size stickRadius 0.4
Changed 14865 bond radii
> view matrix models
> #1,0.99997,0.006983,-0.0045145,-0.3742,-0.0068639,0.99964,0.025862,-3.4086,0.0046935,-0.02583,0.99966,3.6636
> ui mousemode right select
> select clear
> size stickRadius 0.3
Changed 14865 bond radii
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn x 15
> turn y 15
> turn right y 15
Expected an axis vector or a keyword
> turn y -15
Drag select of 7 residues, 2 cryosparc_P986_J74_007_volume_map_sharp.mrc
> select clear
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45 x 45
Expected 'forever' or an integer >= 1 or a keyword
> turn y -45
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -30
> turn y -15
> turn x 30
> select clear
Drag select of 2 residues, 2 cryosparc_P986_J74_007_volume_map_sharp.mrc
> view sel
> select clear
> view orient
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_191_635.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> volume #2 level 0.07
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_191_635_1.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> lighting depthCue false
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> lighting depthCue false
> select clear
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -30
> turn y -15
> select #2
4 models selected
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_191_635_2.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> hide #!2 models
> select /C:635
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:191
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> view
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> lighting depthCue false
> show #!2 models
> view
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> size stickRadius 0.3
Changed 14865 bond radii
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_Pro311_2.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> size stickRadius 0.3
Changed 14865 bond radii
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> size stickRadius 0.3
Changed 14865 bond radii
> hide sel atoms
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> volume #2 level 0.5
> volume #2 level 0.05
> select #2
4 models selected
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 120
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -120
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> volume #2 level 0.045
> volume #2 level 0.065
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> volume #2 level 0.06
> volume #2 level 0.065
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_627_1.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_627_2.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> hide #!1 models
> hide #!2 models
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/cyro-
> EM/cryosparc_P167_J111_007_volume_map_deepemhancer.mrc"
Opened cryosparc_P167_J111_007_volume_map_deepemhancer.mrc as #3, grid size
384,384,384, pixel 0.933, shown at level 0.00141, step 2, values float32
> view
> surface dust #3 size 9.33
> volume #3 level 0.03383
> volume #3 step 1
> show #!1 models
> transparency #3.1 50
> select /B:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> volume #3 level 0.1081
> volume #3 level 0.1689
> volume #3 level 0.06759
> volume #3 level 0.2094
> volume #3 level 0.1317
> volume #3 level 0.1588
> show #!2 models
> select add #3
9 atoms, 8 bonds, 1 residue, 3 models selected
> color #3 #d6d6d6ff models
> transparency (#!1 & sel) 100
> undo
> select subtract #3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3
9 atoms, 8 bonds, 1 residue, 3 models selected
> transparency (#!1 & sel) 100
> select add #1
14493 atoms, 14865 bonds, 3 pseudobonds, 1785 residues, 4 models selected
> select subtract #1
2 models selected
> transparency #3.1 100
> select /B:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> select /A:128
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:211
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:128
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /B:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> hbonds sel reveal true
2 hydrogen bonds found
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> view
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> show #!2 models
> show #!3 models
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> view
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_L128R.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> volume #3 level 0.15
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> select #1/a:105, 128 #1/B:689
26 atoms, 23 bonds, 2 pseudobonds, 3 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select /A:105
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:628
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/a:128,209 #1/B:689
31 atoms, 28 bonds, 2 pseudobonds, 3 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> show #!3 models
> hide #!3 models
> select /A:210
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3 models
> volume #3 level 0.05546
> hide #!3 models
> select /A:131
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!3 models
> hide #!3 models
> select /A:211
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:210
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!3 models
> volume #3 level 0.2074
> hide #!1 models
> show #!1 models
> hide #!3 models
> select clear
> select /A:126
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3 models
> volume #3 level 0.1196
> volume #3 level 0.1399
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> select /A:209
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /A:210
22 atoms, 21 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:126
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> view
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> show #!3 models
> show #!2 models
> volume #3 level 0.15
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> view sel
> view
> view sel
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_128_687.tif"
> width 2400 height 1814 supersample 3 transparentBackground true
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/a:128 #1/B:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_128_687_1.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_128_687_2.tif"
> width 2400 height 1700 supersample 3 transparentBackground true
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_128_687_3.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> view
> hide #!3 models
> hide #!2 models
> show #!1 models
Drag select of 14 atoms, 12 residues, 12 bonds, 2 pseudobonds
> hide sel atoms
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> view
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> ui tool show "Side View"
> view sel
> view
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> show #!2 models
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> zoom 0.5
moved plane near -32.49094805558145 [-0.67568256 0.73435777 -0.06458897]
moved plane far -32.49094805558145 [-0.67568256 0.73435777 -0.06458897]
> view #1/a:311
> zoom 0.5
moved plane near -25.304057897135895 [-0.67568256 0.73435777 -0.06458897]
moved plane far -25.304057897135895 [-0.67568256 0.73435777 -0.06458897]
> ui tool show "Side View"
> view
> view sel
> view
> ui tool show "Side View"
> view #1/a:311
> zoom 0.5
moved plane near -26.607418576936535 [-0.71927312 0.67923814 -0.14588259]
moved plane far -26.607418576936535 [-0.71927312 0.67923814 -0.14588259]
> view #1/a:311
> zoom 0.5
moved plane near -30.487578554483367 [-0.74439055 0.46356651 -0.48061295]
moved plane far -30.487578554483367 [-0.74439055 0.46356651 -0.48061295]
> view all
> view #1/a:311
> zoom 0.5
moved plane near -30.487578554483367 [-0.74439055 0.46356651 -0.48061295]
moved plane far -30.487578554483367 [-0.74439055 0.46356651 -0.48061295]
> view #1/a:311
> zoom 0.5
moved plane near -30.19912538697391 [-0.82657651 0.35324043 -0.43816946]
moved plane far -30.19912538697391 [-0.82657651 0.35324043 -0.43816946]
> focus
Unknown command: focus
> view sel
> view
> select clear
> view #1/a:311
> zoom 0.5
moved plane near -26.53226588750164 [-0.71738105 0.68190248 -0.14273558]
moved plane far -26.53226588750164 [-0.71738105 0.68190248 -0.14273558]
> view
> hide #!1 models
> show #!1 models
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> select clear
> volume #2 level 0.04898
> volume #2 level 0.03897
> volume #2 level 0.05098
> volume #2 level 0.06
> volume #2 level 0.07
> volume #2 level 0.05
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> select clear
> hide #!2 models
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> zoom 0.5
moved plane near -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
moved plane far -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> zoom 0.5
moved plane near -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
moved plane far -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> zoom 0.5
moved plane near -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
moved plane far -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> zoom 0.5
moved plane near -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
moved plane far -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
> show #!2 models
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> zoom 0.5
moved plane near -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
moved plane far -26.53785090117199 [-0.70832847 0.69105875 -0.14390477]
> hide #!2 models
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> zoom 0.5
moved plane near -26.969237706663808 [-0.72653798 0.66561035 -0.17060311]
moved plane far -26.969237706663808 [-0.72653798 0.66561035 -0.17060311]
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_Pro311_3.tif"
> width 2400 height 1683 supersample 3 transparentBackground true
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_Pro311_4.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -43.07107334525739 [-0.19351355 -0.9694981 -0.1504192 ]
moved plane far -43.07107334525739 [-0.19351355 -0.9694981 -0.1504192 ]
> view sel
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -46.37874601958956 [-0.68895397 0.68812654 -0.22764949]
moved plane far -46.37874601958956 [-0.68895397 0.68812654 -0.22764949]
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -46.37874601958956 [-0.68895397 0.68812654 -0.22764949]
moved plane far -46.37874601958956 [-0.68895397 0.68812654 -0.22764949]
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.8
moved plane near -11.594686504897389 [-0.68895397 0.68812654 -0.22764949]
moved plane far -11.594686504897389 [-0.68895397 0.68812654 -0.22764949]
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -46.37874601958956 [-0.68895397 0.68812654 -0.22764949]
moved plane far -46.37874601958956 [-0.68895397 0.68812654 -0.22764949]
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select /A:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -43.96511534529445 [-0.97195904 0.16342458 -0.16907992]
moved plane far -43.96511534529445 [-0.97195904 0.16342458 -0.16907992]
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -43.96511534529445 [-0.97195904 0.16342458 -0.16907992]
moved plane far -43.96511534529445 [-0.97195904 0.16342458 -0.16907992]
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_627_3.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select /C:628
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:105
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -31.524400034387913 [-0.97195904 0.16342458 -0.16907992]
moved plane far -31.524400034387913 [-0.97195904 0.16342458 -0.16907992]
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -29.34552925128724 [-0.75896428 0.64577105 -0.08338445]
moved plane far -29.34552925128724 [-0.75896428 0.64577105 -0.08338445]
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -29.34552925128724 [-0.75896428 0.64577105 -0.08338445]
moved plane far -29.34552925128724 [-0.75896428 0.64577105 -0.08338445]
> turn y -30
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -27.918785900101135 [-0.98055204 0.17795947 -0.08275324]
moved plane far -27.918785900101135 [-0.98055204 0.17795947 -0.08275324]
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -27.591007066500392 [-0.99384117 -0.082603 -0.07386778]
moved plane far -27.591007066500392 [-0.99384117 -0.082603 -0.07386778]
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -29.944170678242532 [-0.93940166 -0.3375362 -0.05994836]
moved plane far -29.944170678242532 [-0.93940166 -0.3375362 -0.05994836]
> turn x 15
> select clear
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -36.40797043665931 [-0.84454141 -0.14715564 -0.51487376]
moved plane far -36.40797043665931 [-0.84454141 -0.14715564 -0.51487376]
> turn x 15
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_191_635_3.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -38.36383580265067 [-0.68537333 -0.11430535 -0.71916455]
moved plane far -38.36383580265067 [-0.68537333 -0.11430535 -0.71916455]
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -29.593182114788473 [-0.76624685 0.64051751 -0.05102002]
moved plane far -29.593182114788473 [-0.76624685 0.64051751 -0.05102002]
> select clear
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -29.593182114788473 [-0.76624685 0.64051751 -0.05102002]
moved plane far -29.593182114788473 [-0.76624685 0.64051751 -0.05102002]
> turn y -90
> undo
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -29.593182114788473 [-0.76624685 0.64051751 -0.05102002]
moved plane far -29.593182114788473 [-0.76624685 0.64051751 -0.05102002]
> turn y -90
> select clear
Drag select of 8 residues
> select /B:643
9 atoms, 8 bonds, 1 residue, 1 model selected
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -28.560395240484922 [-0.71727295 0.69654113 -0.01870552]
moved plane far -28.560395240484922 [-0.71727295 0.69654113 -0.01870552]
> turn y -60
> turn x 30
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_191_635_4.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select /A:191
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /C:635
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:128
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:128
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/a:128 #1/c:689
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -68.78446105095888 [-0.78643574 0.61376632 -0.06935146]
moved plane far -68.78446105095888 [-0.78643574 0.61376632 -0.06935146]
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -44.64232413288556 [-0.78643574 0.61376632 -0.06935146]
moved plane far -44.64232413288556 [-0.78643574 0.61376632 -0.06935146]
> select clear
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -44.64232413288556 [-0.78643574 0.61376632 -0.06935146]
moved plane far -44.64232413288556 [-0.78643574 0.61376632 -0.06935146]
> turn x -45
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -59.09438924543893 [-0.58889464 0.47166871 0.65630146]
moved plane far -59.09438924543893 [-0.58889464 0.47166871 0.65630146]
> turn x -45
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -56.1179828411886 [-0.04638704 0.05327397 0.99750187]
moved plane far -56.1179828411886 [-0.04638704 0.05327397 0.99750187]
> turn x 45
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x 45
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x 45
> view
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x 45
> view
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x -45
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x -45
Drag select of 20 residues
> select clear
Drag select of 3 residues
> view
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x -30
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x -15
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x -15
> view
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn x -30
> turn x -15
> select clear
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -43.68595623658742 [-0.79650824 0.60210283 -0.05519641]
moved plane far -43.68595623658742 [-0.79650824 0.60210283 -0.05519641]
> turn x -30
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -56.13312808154893 [-0.71294444 0.53658046 0.45143269]
moved plane far -56.13312808154893 [-0.71294444 0.53658046 0.45143269]
> turn x -15
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> view
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> view
> select #1/a:128 #1/b:689
20 atoms, 18 bonds, 2 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_128_687_4.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select /B:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:128
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select #1:128, 129, 209, 210, 211, 212
153 atoms, 153 bonds, 18 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> undo
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> select clear
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y +15
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y +15
> volume #3 level 0.1917
> volume #3 level 0.1848
> select clear
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> hide #!3 models
> undo
> hide #!3 models
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> zoom 1.2
moved plane near 10.671148430300462 [-0.98414525 -0.11703363 -0.13327081]
moved plane far 10.671148430300462 [-0.98414525 -0.11703363 -0.13327081]
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 15
> zoom 1.2
moved plane near 10.994553842484653 [-0.97825017 0.14342488 -0.14985245]
moved plane far 10.994553842484653 [-0.97825017 0.14342488 -0.14985245]
> select #1/A:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 15
> zoom 1.2
moved plane near 10.671148495383258 [-0.90568897 0.39410921 -0.15622189]
moved plane far 10.671148495383258 [-0.90568897 0.39410921 -0.15622189]
> select clear
> hide #1/b
> hide #1/b cartoons
> select #1:128, 129, 209, 210, 211, 212
153 atoms, 153 bonds, 18 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> undo
> select #1/a:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_FP_1.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select #1/a:128, 129, 209, 210, 211, 212
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_FP_2.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -42.79155077621475 [-0.90568897 0.39410921 -0.15622189]
moved plane far -42.79155077621475 [-0.90568897 0.39410921 -0.15622189]
> zoom 0.5
moved plane near -85.58309538763106 [-0.90568897 0.39410921 -0.15622189]
moved plane far -85.58309538763106 [-0.90568897 0.39410921 -0.15622189]
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> zoom 0.5
moved plane near -42.79155077621475 [-0.90568897 0.39410921 -0.15622189]
moved plane far -42.79155077621475 [-0.90568897 0.39410921 -0.15622189]
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> view
> show #1/b
> show #1/b cartoons
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 30
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> view sel
> view
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 15
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -30
> select clear
> view
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> select #1/a:105 #1/c:627,628,629
20 atoms, 19 bonds, 4 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_627_4.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> view
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -60
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> select clear
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
Drag select of 43 residues
> select clear
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -60
> select #1/a:191 #1/c:635
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_191_635_5.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> view
> select /C:628
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:105
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel cartoons
> undo
> hide sel atoms
> select /C:635
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:191
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> select #1/a:311
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> view sel
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> color #1 #d6d6d6ff
> show #!3 models
> hide #!2 models
> select #1/a:105-311
1644 atoms, 1685 bonds, 207 residues, 1 model selected
> color sel #0099ccff
> select clear
> color zone #2 near #1 distance 10
> color zone #3 near #1 distance 10
> volume #3 level 0.06
> volume #3 level 0.07
> volume #3 level 0.08
> volume #3 level 0.07
> volume #3 level 0.08
> volume #3 level 0.06
> volume #3 level 0.2
> volume #3 level 0.1
> volume #3 level 0.7
> volume #3 level 0.07
> volume #3 level 0.1
> volume #3 level 0.7
> volume #3 level 0.08
> volume #3 level 0.1
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> select /A:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #1/a:2000, 2001, 2011
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel #0099ccff
> color zone #1 near #3 distance 10
color zone: No surfaces specified.
> color zone #3 near #1 distance 10
> color zone #3 near #1 distance 15
> hide #!1 models
> show #!1 models
> volume splitbyzone #3
Opened cryosparc_P167_J111_007_volume_map_deepemhancer.mrc 0 as #4.1, grid
size 384,384,384, pixel 0.933, shown at level 0.1, step 1, values float32
Opened cryosparc_P167_J111_007_volume_map_deepemhancer.mrc 1 as #4.2, grid
size 384,384,384, pixel 0.933, shown at level 0.1, step 1, values float32
Opened cryosparc_P167_J111_007_volume_map_deepemhancer.mrc 2 as #4.3, grid
size 384,384,384, pixel 0.933, shown at level 0.1, step 1, values float32
> hide #!4.2 models
> hide #!1 models
> surface dust #4.1 size 9.33
> surface dust #4.3 size 9.33
> volume #4.3 level 0.03788
> show #!1 models
> volume #4.3 level 0.05
> volume #4.3 level 0.7
> volume #4.3 level 0.06
> volume #4.3 level 0.07
> volume #4.3 level 0.08
> volume #4.3 level 0.1
> volume #4.3 level 0.7
> volume #4.3 level 0.07
> transparency #4.1.1#4.3.1 0
> transparency #4.1.1#4.3.1 50
> volume #4.3 level 0.1
> volume #4.3 level 0.15
> select clear
> hide #!1 models
> transparency #4.1.1#4.3.1 0
> show #!1 models
> hide #!1 models
> show #!1 models
> transparency #4.1.1#4.3.1 50
> hide #!1 models
> view #4.3
> transparency #4.1.1#4.3.1 0
> show #!1 models
> volume #4.1 level 0.1277
> hide #!1 models
> volume #4.3 level 0.1
> volume #4.3 level 0.15
> volume #4.3 level 0.1
> view #4.3
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_DI_local_refinement_1.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> turn y 180
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_DI_local_refinement_2.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> turn y 180
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250715_KSHV_prefuison_gB_model_DI_local_refinement_3.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> undo
> hide #!4.3 models
> close #4
> view
> select #1:53-78, 511-617
2973 atoms, 3027 bonds, 372 residues, 1 model selected
> color sel #cc9900ff
> select #1:79-92, 456-510
1743 atoms, 1779 bonds, 207 residues, 1 model selected
> color sel #ccff00ff
> select #1:93-104, 312-409
2571 atoms, 2643 bonds, 330 residues, 1 model selected
> color sel #33cc66ff
> select #1:105-311
4932 atoms, 5055 bonds, 621 residues, 1 model selected
> color sel #0099ccff
> select #1:618-690
1770 atoms, 1797 bonds, 219 residues, 1 model selected
> color sel #ff0000ff
> select clear
> select #1
14493 atoms, 14865 bonds, 5 pseudobonds, 1785 residues, 3 models selected
> select #1
14493 atoms, 14865 bonds, 5 pseudobonds, 1785 residues, 3 models selected
> hide sel atoms
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 30
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -30
> ui tool show "Side View"
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> undo
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_109_628_635.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 15
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 15
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_109_628_635_1.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -5
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -5
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> view
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -30
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y 15
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> view
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -30
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -15
> select clear
> view
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> turn y -45
> select clear
> select #1/a:105, 191 #1/c:627, 628, 629, 635
32 atoms, 30 bonds, 6 residues, 1 model selected
> show sel atoms
> view sel
> color sel byhetero
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Figures/Figure3/250712_KSHV_prefuison_gB_model_105_109_628_635_2.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> undo
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/Cryo-
> EM/cryosparc_P211_J111_008_volume_map_half_A_deepEMhancer-
> sharpened_flipped.mrc"
Opened cryosparc_P211_J111_008_volume_map_half_A_deepEMhancer-
sharpened_flipped.mrc as #1, grid size 384,384,384, pixel 0.933, shown at
level 0.0024, step 2, values float32
> set bgColor white
> surface dust #1 size 9.33
> volume #1 level 0.01737
> volume #1 step 1
> graphics silhouettes true
> volume #1 level 0.135
> surface dust #1 size 9.33
> cd "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures"
Current working directory is: /Users/kjyeol/Library/CloudStorage/Box-
Box/JeongRyeolKim/project/HSV-2 prefusion gB specific mAbs/figures
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures/071625_HSV2_G3_5-18_deepemhancer_map.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific
> mAbs/Modeling/RealSpaceRefine_22/250710_HSV2_G3_5-18_complex_5_real_space_refined_022.pdb"
Chain information for 250710_HSV2_G3_5-18_complex_5_real_space_refined_022.pdb
#2
---
Chain | Description
A B C | No description available
D F H | No description available
E G I | No description available
> select add #2
38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
38337 atoms, 38826 bonds, 9 pseudobonds, 2454 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> hide #!1 models
> ui mousemode right select
> select clear
> select #1/a,b,c
Nothing selected
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #d6d6d6ff
> color (#!2 & sel) #c0c0c0ff
> lighting soft
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #ff40ffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #9437ffff
> color (#!2 & sel) #76d6ffff
> color (#!2 & sel) #7a81ffff
> color (#!2 & sel) #d783ffff
> color (#!2 & sel) #7a81ffff
> color (#!2 & sel) #ff85ffff
> color (#!2 & sel) #ff8ad8ff
> color (#!2 & sel) #76d6ffff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #73fcd6ff
> color (#!2 & sel) #73fdffff
> color (#!2 & sel) #ff40ffff
> color (#!2 & sel) #ff2f92ff
> color (#!2 & sel) #0433ffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #00fa92ff
> color (#!2 & sel) #00f900ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #005493ff
> color (#!2 & sel) #531b93ff
> color (#!2 & sel) #942193ff
> color (#!2 & sel) #941751ff
> color (#!2 & sel) #531b93ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #009193ff
> color (#!2 & sel) #009051ff
> color (#!2 & sel) #008f00ff
> color (#!2 & sel) #919191ff
> color (#!2 & sel) #a9a9a9ff
> color (#!2 & sel) #c0c0c0ff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #d6d6d6ff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #c0c0c0ff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #ffffffff
[Repeated 1 time(s)]
> color (#!2 & sel) #ffffff54
> color (#!2 & sel) #ffffff55
> color (#!2 & sel) #ffffffdc
> color (#!2 & sel) #ffffffec
> color (#!2 & sel) #fffffffc
> color (#!2 & sel) #ffffffff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #d6d6d6ff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #5e5e5eff
> color (#!2 & sel) #797979ff
> color (#!2 & sel) #919191ff
> color (#!2 & sel) #929292ff
> color (#!2 & sel) #009193ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #531b93ff
> color (#!2 & sel) #942193ff
> color (#!2 & sel) #941751ff
> color (#!2 & sel) #ff9300ff
> color (#!2 & sel) #fffb00ff
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #00f900ff
> color (#!2 & sel) #8efa00ff
> color (#!2 & sel) #0433ffff
> color (#!2 & sel) #ff2f92ff
> color (#!2 & sel) #ff7e79ff
> color (#!2 & sel) #fffc79ff
> color (#!2 & sel) #d783ffff
> color (#!2 & sel) #7a81ffff
> color (#!2 & sel) #76d6ffff
> select clear
> select #2/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!2 & sel) #ff8ad8ff
> color (#!2 & sel) #ff85ffff
> color (#!2 & sel) #d783ffff
> color (#!2 & sel) #7a81ffff
> color (#!2 & sel) #ff40ffff
> color (#!2 & sel) #9437ffff
> color (#!2 & sel) #0433ffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #00fa92ff
> color (#!2 & sel) #00f900ff
> color (#!2 & sel) #8efa00ff
> color (#!2 & sel) #fffb00ff
> color (#!2 & sel) #d6d6d6ff
> color (#!2 & sel) #ebebebff
> color (#!2 & sel) #ffffffff
> color (#!2 & sel) #ebebebff
> color (#!2 & sel) #d6d6d6ff
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures/071625_HSV2_G3_5-18_complex_model.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> cartoon style width 2.5 thickness 1
> select clear
[Repeated 2 time(s)]
> cartoon style width 2.5 thickness 0.5
> cartoon style width 2.5 thickness 0.8
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures/071625_HSV2_G3_5-18_complex_model_1.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures/071625_HSV2_G3_5-18_complex_model_2.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific
> mAbs/Structure/250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb"
Chain information for 250709_HSV2_G3_5-18_complex_8_real_space_refined_019.pdb
#3
---
Chain | Description
A B C | No description available
D F H | No description available
E G I | No description available
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!3 cartoons
> hide #!3 atoms
> show #!2 models
> hide #!2 models
> cartoon style width 2.5 thickness 0.8
> lighting soft
> select #3/b,c
18592 atoms, 18829 bonds, 6 pseudobonds, 1176 residues, 2 models selected
> select #3/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!3 & sel) #ebebebff
> color (#!3 & sel) #d6d6d6ff
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures/071625_HSV2_G3_5-18_complex_model_3.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific
> mAbs/Structure/250709_HSV2_G3_5-18_complex_5_real_space_refined_017.pdb"
Chain information for 250709_HSV2_G3_5-18_complex_5_real_space_refined_017.pdb
#4
---
Chain | Description
A B C | No description available
D F H | No description available
E G I | No description available
> show #!3-4 cartoons
> hide #!3-4 atoms
> hide #!3 models
> cartoon style width 2.5 thickness 0.8
> select #4/a,b,c
27888 atoms, 28245 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color (#!4 & sel) #ffffffff
> color (#!4 & sel) #d6d6d6ff
> select clear
> save "/Users/kjyeol/Library/CloudStorage/Box-Box/JeongRyeolKim/project/HSV-2
> prefusion gB specific mAbs/figures/071625_HSV2_G3_5-18_complex_model_4.tif"
> width 2400 height 2400 supersample 3 transparentBackground true
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63KH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 8 days, 10 hours, 33 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG ULTRAGEAR:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
narwhals: 1.35.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.5
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
plotly: 6.0.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.3
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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