The following bug report has been submitted:
Platform: macOS-15.6.1-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff8503e3f80 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1238 in draw_background
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/camera.py", line 195 in draw_background
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 239 in _draw_scene
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 52)
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{
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"incident" : "F35698E7-B08B-4C23-B4AF-DF4E6BB50941",
"pid" : 22131,
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"bug_type" : "309",
"procLaunch" : "2025-09-01 17:24:49.0342 +1000",
"procStartAbsTime" : 90917842214561,
"procExitAbsTime" : 606278965968208,
"procName" : "ChimeraX",
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"appleIntelligenceStatus" : {"reasons":["deviceNotCapable"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"sleepWakeUUID" : "3F096030-32B2-44BE-A981-24D9C8D03F05",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":22131},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics kernel error: 0x0ed785f9\n"],
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"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 22353044,
"uuid" : "fe1f4402-834c-30cb-b66b-ccec88c1dc60",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.70.52"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703370043392,
"size" : 632520,
"uuid" : "c6e52c5e-d1d2-354c-a4ec-069f8d5baafe",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703392567296,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14621538,
"uuid" : "1116522e-84bc-3b5d-863d-60d4c5ce0001",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3603"
}
],
"sharedCache" : {
"base" : 140703341568000,
"size" : 30064771072,
"uuid" : "1fc10b1e-bb3a-3634-a370-8a2e7d0fdf8a"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "34bbb3acf03d78c8e9c22d6f52c28c1f0ab0e0df",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "67648e5334a82511f4acf879",
"factorPackIds" : {
},
"deploymentId" : 240000008
}
],
"experiments" : [
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6DDE
Summary of feedback from opening 6DDE fetched from pdb
---
notes | Fetching compressed mmCIF 6dde from http://files.rcsb.org/download/6dde.cif
Fetching CCD ETA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/ETA/ETA.cif
Fetching CCD MEA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/MEA/MEA.cif
6dde title:
μ Opioid Receptor-Gi Protein Complex [more info...]
Chain information for 6dde #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
D | DAMGO |
E | scFv16 |
R | Mu-type opioid receptor | OPRM_MOUSE 3-358
Non-standard residues in 6dde #1
---
ETA — ethanolamine
> hide atoms
> show cartoons
> close session
> open 5uz7
Summary of feedback from opening 5uz7 fetched from pdb
---
note | Fetching compressed mmCIF 5uz7 from http://files.rcsb.org/download/5uz7.cif
5uz7 title:
Volta phase plate cryo-electron microscopy structure of a calcitonin receptor-
heterotrimeric Gs protein complex [more info...]
Chain information for 5uz7 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-68
N | NANOBODY 35 |
R | Calcitonin receptor | CALCR_HUMAN 25-474
> style stick
Changed 7643 atom styles
> show cartoons
> select /R
2106 atoms, 2167 bonds, 3 pseudobonds, 266 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> hide atoms
> set bgColor white
> select /A
1566 atoms, 1596 bonds, 5 pseudobonds, 185 residues, 2 models selected
> color (#!1 & sel) #fffeeaff
> color (#!1 & sel) #fffae5ff
> color (#!1 & sel) #fff2dcff
> color (#!1 & sel) #ffd6c1ff
> color (#!1 & sel) #ffcdb8ff
> color (#!1 & sel) #ffb199ff
> color (#!1 & sel) #ffa78eff
> color (#!1 & sel) #ff9f85ff
> color (#!1 & sel) #ff9a7fff
> color (#!1 & sel) #ff9075ff
> color (#!1 & sel) #ff8567ff
> color (#!1 & sel) #ff8163ff
> color (#!1 & sel) #ff8061ff
> color (#!1 & sel) #ff7e5eff
> color (#!1 & sel) #ff7b58ff
> color (#!1 & sel) #ff7a56ff
> color (#!1 & sel) #ff7a54ff
> color (#!1 & sel) #ff7a55ff
> color (#!1 & sel) #ff7c57ff
> color (#!1 & sel) #ff805dff
> color (#!1 & sel) #ff8260ff
> color (#!1 & sel) #ff8361ff
> color (#!1 & sel) #ff8b69ff
> color (#!1 & sel) #ff8f6cff
> color (#!1 & sel) #ff906dff
> color (#!1 & sel) #ff906eff
> color (#!1 & sel) #ff916eff
> color (#!1 & sel) #ff906cff
> color (#!1 & sel) #ff9068ff
> color (#!1 & sel) #ff9067ff
> color (#!1 & sel) #ff9165ff
> color (#!1 & sel) #ff9362ff
> color (#!1 & sel) #ff9361ff
> color (#!1 & sel) #ff9360ff
> color (#!1 & sel) #ff935fff
> color (#!1 & sel) #ff935eff
> color (#!1 & sel) #ff925eff
> color (#!1 & sel) #ff915dff
> color (#!1 & sel) #ff905cff
> color (#!1 & sel) #ff935fff
> color (#!1 & sel) #ff9661ff
> color (#!1 & sel) #ffaa76ff
> color (#!1 & sel) #ffad7bff
> color (#!1 & sel) #ffad7cff
> color (#!1 & sel) #ffae7eff
> color (#!1 & sel) #ffb080ff
> color (#!1 & sel) #ffb081ff
> color (#!1 & sel) #ffb180ff
> color (#!1 & sel) #ffb37cff
> color (#!1 & sel) #ffb37bff
> color (#!1 & sel) #ffb279ff
> color (#!1 & sel) #ffb075ff
> color (#!1 & sel) #ffad71ff
> color (#!1 & sel) #ffac70ff
> color (#!1 & sel) #ffab6fff
> color (#!1 & sel) #ffa96eff
> color (#!1 & sel) #ffa96dff
> color (#!1 & sel) #ffa86cff
> color (#!1 & sel) #ffa66bff
> color (#!1 & sel) #ffa368ff
> color (#!1 & sel) #ffa367ff
> color (#!1 & sel) #ffa065ff
> color (#!1 & sel) #ff9e64ff
> color (#!1 & sel) #ff9e63ff
> color (#!1 & sel) #ff985dff
> color (#!1 & sel) #ff975dff
> color (#!1 & sel) #ff935fff
> color (#!1 & sel) #ff9360ff
> color (#!1 & sel) #ff9260ff
> color (#!1 & sel) #ff9160ff
> color (#!1 & sel) #ff915fff
> color (#!1 & sel) #ff8f60ff
> color (#!1 & sel) #ff8d61ff
> color (#!1 & sel) #ff8c62ff
> color (#!1 & sel) #ff8c63ff
> color (#!1 & sel) #ff8d64ff
> color (#!1 & sel) #ff8e68ff
> color (#!1 & sel) #ff8f6aff
> color (#!1 & sel) #ff906bff
> color (#!1 & sel) #ff906dff
> color (#!1 & sel) #ff906fff
> color (#!1 & sel) #ff9070ff
> color (#!1 & sel) #ff9071ff
> color (#!1 & sel) #ff8f71ff
> color (#!1 & sel) #ff8e72ff
> color (#!1 & sel) #ff8b6eff
> color (#!1 & sel) #ff8668ff
> color (#!1 & sel) #ff8567ff
> color (#!1 & sel) #ff8566ff
> color (#!1 & sel) #ff8061ff
> color (#!1 & sel) #ff7c5dff
> color (#!1 & sel) #ff7a5aff
> color (#!1 & sel) #ff7656ff
> color (#!1 & sel) #ff7454ff
> color (#!1 & sel) #ff7453ff
> color (#!1 & sel) #ff7352ff
> open 6dde
6dde title:
μ Opioid Receptor-Gi Protein Complex [more info...]
Chain information for 6dde #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
D | DAMGO |
E | scFv16 |
R | Mu-type opioid receptor | OPRM_MOUSE 3-358
Non-standard residues in 6dde #2
---
ETA — ethanolamine
> select add #1
5537 atoms, 5642 bonds, 5 pseudobonds, 708 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> style #!2 stick
Changed 8489 atom styles
> hide #!2 atoms
> show #!2 cartoons
> select #2/D
37 atoms, 38 bonds, 5 residues, 1 model selected
> select #2/R
2097 atoms, 2148 bonds, 281 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/D
37 atoms, 38 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> tile
2 models tiled
> select #2/A
1679 atoms, 1708 bonds, 2 pseudobonds, 217 residues, 2 models selected
> color (#!2 & sel) #ff7352ff
> select #1/B#2/B
5126 atoms, 5220 bonds, 676 residues, 2 models selected
> color sel #ff9466ff
> color sel #ff9669ff
> color sel #ff9c70ff
> color sel #ffa478ff
> color sel #ffdbb2ff
> color sel #fdffd2ff
> color sel #f7ffd5ff
> color sel #e3ffd7ff
> color sel #dbffd6ff
> color sel #d4ffd6ff
> color sel #d2ffddff
> color sel #d0ffdeff
> color sel #cbffe0ff
> color sel #c5ffe1ff
> color sel #beffe1ff
> color sel #b8ffe1ff
> color sel #b5ffe1ff
> color sel #b3ffe1ff
> color sel #adffe1ff
> color sel #a8ffe0ff
> color sel #a6ffe0ff
> color sel #a1ffddff
> color sel #9effdaff
> color sel #96ffd4ff
> color sel #90ffd2ff
> color sel #8dffd0ff
> color sel #8cffcfff
> color sel #8affcdff
> color sel #89ffccff
> color sel #88ffccff
> color sel #87ffcaff
> color sel #88ffcaff
> color sel #88ffcdff
> color sel #88ffcfff
> color sel #89ffdbff
> color sel #8affe4ff
> color sel #8cffe9ff
> color sel #8cfff4ff
> color sel #8dfff8ff
> color sel #8efffeff
> color sel #8ffaffff
> color sel #90f4ffff
> color sel #90efffff
> color sel #8feaffff
> color sel #8ce1ffff
> color sel #8bdfffff
> color sel #8adeffff
> color sel #8adcffff
> color sel #88d8ffff
> color sel #86d4ffff
> color sel #84cfffff
> color sel #83ceffff
> color sel #7fc7ffff
> color sel #7ec4ffff
> color sel #79bfffff
> color sel #74baffff
> color sel #72b8ffff
> color sel #6db5ffff
> color sel #6ab2ffff
> color sel #68b0ffff
> color sel #64aeffff
> color sel #5faaffff
> color sel #5ca9ffff
> color sel #59a6ffff
> color sel #57a4ffff
> color sel #56a4ffff
> color sel #55a2ffff
> color sel #54a1ffff
> color sel #4e9dffff
> color sel #4999ffff
> color sel #4898ffff
> color sel #4696ffff
> color sel #4697ffff
> color sel #4898ffff
> color sel #4f9affff
> color sel #549cffff
> color sel #599dffff
> color sel #5d9effff
> color sel #659fffff
> color sel #689fffff
> color sel #699fffff
> color sel #6aa0ffff
> color sel #6ba0ffff
> color sel #6da0ffff
> color sel #70a1ffff
> color sel #71a1ffff
> color sel #73a2ffff
> color sel #74a2ffff
> color sel #75a2ffff
> color sel #77a2ffff
> color sel #7ba4ffff
> color sel #7da5ffff
> color sel #7fa6ffff
> color sel #80a7ffff
> color sel #82a9ffff
> color sel #83aaffff
> color sel #84acffff
> color sel #86aeffff
> color sel #87afffff
> color sel #89b1ffff
> color sel #8ab3ffff
> color sel #8bb3ffff
> color sel #8cb4ffff
> color sel #8db5ffff
> color sel #8db6ffff
> color sel #8eb6ffff
> color sel #8eb9ffff
> color sel #8fbbffff
> color sel #8fbcffff
> color sel #90c1ffff
> color sel #90c3ffff
> color sel #90c4ffff
> color sel #8dc5ffff
> color sel #8bc6ffff
> color sel #85c7ffff
> color sel #80c7ffff
> color sel #7cc7ffff
> color sel #7bc7ffff
> color sel #7ac7ffff
> color sel #7ac8ffff
> color sel #79c8ffff
> color sel #77c8ffff
> color sel #73c7ffff
> color sel #6dc6ffff
> color sel #6ac5ffff
> color sel #68c4ffff
> color sel #69c5ffff
> color sel #69c6ffff
> color sel #69c7ffff
> color sel #6acaffff
> color sel #6acbffff
> color sel #6accffff
> color sel #6cd0ffff
> color sel #78d8ffff
> color sel #83deffff
> color sel #84deffff
> color sel #85deffff
> color sel #8cdeffff
> color sel #90deffff
> color sel #97deffff
> color sel #99deffff
> color sel #9dddffff
> color sel #9fdcffff
> color sel #a0dbffff
> color sel #a2d3ffff
> color sel #a3d2ffff
> color sel #a3d0ffff
> color sel #a3ceffff
> color sel #a3cdffff
> color sel #a4cdffff
> color sel #a6ccffff
> color sel #a8ccffff
> color sel #aacbffff
> color sel #abcbffff
> color sel #abcaffff
> color sel #abc9ffff
> color sel #abc6ffff
> color sel #aac5ffff
> color sel #aac4ffff
> color sel #abc2ffff
> color sel #abc0ffff
> color sel #aabdffff
> color sel #aabcffff
> color sel #a9baffff
> color sel #a8b8ffff
> color sel #a4b3ffff
> color sel #a3b1ffff
> color sel #a2b1ffff
> color sel #a1b0ffff
> color sel #9fafffff
> color sel #9daeffff
> color sel #9baeffff
> color sel #9aadffff
> color sel #9aacffff
> color sel #99acffff
> color sel #98acffff
> color sel #98abffff
> color sel #97abffff
> color sel #97aaffff
> color sel #96aaffff
> color sel #95a9ffff
> color sel #94a9ffff
> color sel #94a8ffff
> color sel #92a8ffff
> color sel #8fa7ffff
> color sel #8ea6ffff
> color sel #8ba6ffff
> color sel #7ea2ffff
> color sel #779fffff
> color sel #719effff
> color sel #6e9cffff
> color sel #6a9bffff
> color sel #689bffff
> color sel #679bffff
> color sel #659affff
> color sel #6299ffff
> color sel #6199ffff
> color sel #6198ffff
> color sel #6098ffff
> color sel #6198ffff
> color sel #6298ffff
> color sel #6398ffff
> color sel #6499ffff
> color sel #6599ffff
> color sel #679affff
> color sel #689affff
> color sel #6a9bffff
> color sel #6c9cffff
> color sel #709cffff
> color sel #749effff
> color sel #759fffff
> color sel #769fffff
> color sel #7aa0ffff
> color sel #7da2ffff
> color sel #85a7ffff
> color sel #8dadffff
> color sel #90afffff
> color sel #91b0ffff
> color sel #93b1ffff
> color sel #95b2ffff
> color sel #97b3ffff
> color sel #99b4ffff
> color sel #9ab5ffff
> color sel #9cb6ffff
> color sel #9eb8ffff
> color sel #a0b9ffff
> color sel #a1b9ffff
> color sel #a0b8ffff
> color sel #9eb7ffff
> color sel #9cb5ffff
> color sel #99b2ffff
> color sel #92acffff
> color sel #6b91ffff
> color sel #6891ffff
> color sel #6790ffff
> color sel #658effff
> color sel #628dffff
> color sel #618cffff
> color sel #5f8affff
> color sel #5d88ffff
> color sel #5e89ffff
> color sel #5f8affff
> color sel #628cffff
> color sel #638cffff
> color sel #648dffff
> color sel #648effff
> color sel #658effff
> color sel #668effff
> color sel #668fffff
> color sel #678fffff
> color sel #688fffff
> color sel #6990ffff
> color sel #6a90ffff
> select #1/G#2/C
801 atoms, 813 bonds, 108 residues, 2 models selected
> color sel #b79cffff
> color sel #bc9effff
> color sel #c59fffff
> color sel #cba0ffff
> color sel #d39fffff
> color sel #d59dffff
> color sel #d89bffff
> color sel #d89affff
> color sel #da99ffff
> color sel #de98ffff
> color sel #df97ffff
> color sel #e097ffff
> color sel #e296ffff
> color sel #e594ffff
> color sel #e692ffff
> color sel #e792ffff
> color sel #e892ffff
> color sel #ea92ffff
> color sel #eb92ffff
> color sel #ec92ffff
> color sel #e691ffff
> color sel #df8dffff
> color sel #da89ffff
> color sel #d686ffff
> color sel #d485ffff
> color sel #d384ffff
> color sel #d182ffff
> color sel #cf80ffff
> color sel #cd7fffff
> color sel #cc7effff
> color sel #c77cffff
> color sel #c378ffff
> color sel #c074ffff
> color sel #bf73ffff
> color sel #be72ffff
> color sel #bd70ffff
> color sel #bd6effff
> color sel #bc6dffff
> color sel #bc6effff
> color sel #be72ffff
> color sel #bf76ffff
> color sel #c079ffff
> color sel #c17cffff
> color sel #c27effff
> color sel #c382ffff
> color sel #c483ffff
> color sel #c584ffff
> color sel #c586ffff
> color sel #c688ffff
> color sel #c78affff
> color sel #c78bffff
> color sel #c88fffff
> color sel #ca93ffff
> color sel #cb96ffff
> color sel #cc99ffff
> color sel #cf9dffff
> color sel #d09fffff
> color sel #d0a1ffff
> color sel #d1a2ffff
> color sel #d1a3ffff
> color sel #d2a4ffff
> color sel #d2a5ffff
> color sel #d3a8ffff
> color sel #d4a9ffff
> color sel #d2a6ffff
> color sel #d1a5ffff
> color sel #d0a4ffff
> color sel #ce9effff
> color sel #ca97ffff
> color sel #c68fffff
> color sel #bf7dffff
> color sel #bb75ffff
> color sel #ba72ffff
> color sel #b96effff
> color sel #b86cffff
> color sel #b76affff
> color sel #b565ffff
> color sel #b563ffff
> color sel #b360ffff
> color sel #b25effff
> color sel #b25cffff
> color sel #b15affff
> color sel #b059ffff
> color sel #b058ffff
> color sel #b057ffff
> color sel #af57ffff
> select #1/N
972 atoms, 994 bonds, 128 residues, 1 model selected
> color sel #ffacbfff
> color sel #ffabbcff
> color sel #ffa7b3ff
> color sel #ffa5afff
> color sel #ffa3acff
> color sel #ffa0a5ff
> color sel #ff9fa2ff
> color sel #ff9ea0ff
> color sel #ff9e9eff
> color sel #ff9f9dff
> color sel #ffa09dff
> color sel #ffa39eff
> color sel #ffa69eff
> color sel #ffaa9fff
> color sel #ffab9fff
> color sel #ffb1a1ff
> color sel #ffbea2ff
> color sel #ffc5a2ff
> color sel #ffcfa2ff
> color sel #ffd1a1ff
> color sel #ffd4a0ff
> color sel #ffd5a0ff
> color sel #ffd69fff
> color sel #ffd79fff
> color sel #ffda9fff
> color sel #ffdc9eff
> color sel #ffdf9dff
> color sel #ffe19cff
> color sel #ffe39aff
> color sel #ffe697ff
> color sel #ffe696ff
> color sel #ffe795ff
> color sel #ffe794ff
> color sel #ffe891ff
> color sel #ffe890ff
> color sel #ffe88fff
> color sel #ffe88eff
> color sel #ffe88dff
> color sel #ffe88aff
> color sel #ffe687ff
> color sel #ffe583ff
> color sel #ffe380ff
> color sel #ffe27cff
> color sel #ffe07aff
> color sel #ffdf76ff
> color sel #ffde74ff
> color sel #ffdd72ff
> color sel #ffdd71ff
> color sel #ffdd70ff
> color sel #ffdc71ff
> color sel #ffdc70ff
> color sel #ffdb70ff
> color sel #ffda71ff
> color sel #ffd773ff
> color sel #ffd673ff
> color sel #ffd674ff
> color sel #ffd876ff
> color sel #ffd977ff
> color sel #ffda79ff
> color sel #ffdc7aff
> color sel #ffe17bff
> color sel #fff080ff
> color sel #fff381ff
> color sel #fff883ff
> color sel #fff984ff
> color sel #fffa84ff
> color sel #fffd87ff
> color sel #feff8cff
> color sel #fcff8fff
> color sel #fcff91ff
> color sel #fcff93ff
> color sel #fcff97ff
> color sel #fcff99ff
> color sel #fdff9bff
> color sel #feff9eff
> color sel #ffffa0ff
> color sel #ffffa1ff
> color sel #ffffa2ff
> color sel #ffffa3ff
> color sel #fffea3ff
> color sel #fffea4ff
> color sel #fffea5ff
> color sel #fffda6ff
> color sel #fffda7ff
> color sel #fffda8ff
> color sel #fffca7ff
> color sel #fffca6ff
> color sel #fffba6ff
> color sel #fffba5ff
> color sel #fff9a3ff
> color sel #fff5a1ff
> color sel #fff3a0ff
> color sel #fff09fff
> color sel #ffee9dff
> color sel #ffe99aff
> color sel #ffe89aff
> select #2/E
1748 atoms, 1794 bonds, 1 pseudobond, 232 residues, 2 models selected
> color (#!2 & sel) #fffeafff
> color (#!2 & sel) #efffb6ff
> color (#!2 & sel) #d3ffb7ff
> color (#!2 & sel) #cdffb6ff
> color (#!2 & sel) #c3ffb4ff
> color (#!2 & sel) #bdffb3ff
> color (#!2 & sel) #b2ffb2ff
> color (#!2 & sel) #b1ffb7ff
> color (#!2 & sel) #afffb9ff
> color (#!2 & sel) #adffbaff
> color (#!2 & sel) #a8ffbdff
> color (#!2 & sel) #a5ffc1ff
> color (#!2 & sel) #a2ffc4ff
> color (#!2 & sel) #9fffc6ff
> color (#!2 & sel) #9cffc8ff
> color (#!2 & sel) #9bffc8ff
> color (#!2 & sel) #99ffc8ff
> color (#!2 & sel) #96ffc9ff
> color (#!2 & sel) #94ffc9ff
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> color (#!2 & sel) #40bf6eff
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> color (#!2 & sel) #42bf71ff
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> color (#!2 & sel) #44bf74ff
> color (#!2 & sel) #45c275ff
> color (#!2 & sel) #45c477ff
> color (#!2 & sel) #46c678ff
> color (#!2 & sel) #47c779ff
> color (#!2 & sel) #47c879ff
> color (#!2 & sel) #47c97aff
> color (#!2 & sel) #48ca7bff
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> color (#!2 & sel) #4ad07eff
> color (#!2 & sel) #4ad17eff
> color (#!2 & sel) #4ad27fff
> color (#!2 & sel) #4bd481ff
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> color (#!2 & sel) #4cd883ff
> color (#!2 & sel) #4bd581ff
> color (#!2 & sel) #4bd380ff
> color (#!2 & sel) #4ad07eff
> color (#!2 & sel) #49cd7cff
> color (#!2 & sel) #48ca7bff
> color (#!2 & sel) #47c97aff
> color (#!2 & sel) #47c979ff
> color (#!2 & sel) #47c879ff
> color (#!2 & sel) #46c678ff
> color (#!2 & sel) #46c578ff
> color (#!2 & sel) #46c577ff
> color (#!2 & sel) #46c578ff
> ui mousemode right select
> select clear
> select #1/N
972 atoms, 994 bonds, 128 residues, 1 model selected
> color sel #46c678ff
> color sel #49ce7dff
> color sel #54ed90ff
> color sel #5aff9aff
> color sel #56ff94ff
> color sel #59ff93ff
> color sel #60ff8fff
> color sel #6dff86ff
> color sel #78ff7aff
> color sel #a1ff81ff
> color sel #aaff82ff
> color sel #b2ff82ff
> color sel #b8ff82ff
> color sel #bbff82ff
> color sel #bcff81ff
> color sel #bfff81ff
> color sel #c2ff80ff
> color sel #c5ff7fff
> color sel #c7ff7fff
> color sel #ceff7dff
> color sel #d4ff7cff
> color sel #d8ff7bff
> color sel #d9ff7aff
> color sel #dfff79ff
> color sel #e6ff76ff
> color sel #eaff75ff
> color sel #eeff74ff
> color sel #f1ff73ff
> color sel #f3ff72ff
> color sel #fdff6fff
> color sel #fff96eff
> color sel #fff66dff
> color sel #fff36dff
> color sel #fff06eff
> color sel #ffec70ff
> color sel #ffea70ff
> color sel #ffe871ff
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> color sel #ffe372ff
> color sel #ffe173ff
> color sel #ffe073ff
> color sel #ffde72ff
> color sel #ffdd72ff
> color sel #ffdc71ff
> color sel #ffda70ff
> color sel #ffd86eff
> color sel #ffd36aff
> color sel #ffd269ff
> color sel #ffd067ff
> color sel #ffce65ff
> color sel #ffcb61ff
> color sel #ffcb60ff
> color sel #ffca5fff
> color sel #ffc95eff
> color sel #ffc85dff
> color sel #ffc75bff
> color sel #ffc658ff
> color sel #ffc455ff
> color sel #ffc454ff
> color sel #ffc352ff
> color sel #ffc252ff
> color sel #ffc251ff
> color sel #ffc350ff
> color sel #ffc351ff
> color sel #ffc350ff
> color sel #ffc351ff
> color sel #ffc451ff
> color sel #ffc551ff
> color sel #ffc651ff
> color sel #ffc750ff
> color sel #ffc74fff
> color sel #ffc84fff
> color sel #ffc84eff
> color sel #ffc94eff
> color sel #ffc84eff
> color sel #ffc94fff
> color sel #ffc950ff
> color sel #ffc951ff
> color sel #ffc952ff
> color sel #ffca53ff
> color sel #ffca54ff
> color sel #ffca55ff
> color sel #ffcb55ff
> select clear
> hide #!2 models
> ui tool show "Side View"
> cartoon style helix width 1.0 thickness 0.2
> cartoon style helix width 1.0 thickness 0.4
> cartoon style helix width 1.3 thickness 0.4
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> lighting full
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> show #!2 models
> graphics silhouettes width 1.3 depthJump 0.1
> save "/Users/dongju/Desktop/Research projects-
> Monash/Thesis_DL/Figures/Chapter1/Nb35.png" width 1500 height 1177
> supersample 3 transparentBackground true
> select clear
> hide #!1 models
> save "/Users/dongju/Desktop/Research projects-
> Monash/Thesis_DL/Figures/Chapter1/Scfv16.png" width 1500 height 1177
> supersample 3 transparentBackground true
> open 6G79
Summary of feedback from opening 6G79 fetched from pdb
---
notes | Fetching compressed mmCIF 6g79 from http://files.rcsb.org/download/6g79.cif
Fetching CCD EP5 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/EP5/EP5.cif
6g79 title:
Coupling specificity of heterotrimeric Go to the serotonin 5-HT1B receptor
[more info...]
Chain information for 6g79 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(o) subunit alpha | GNAO_HUMAN 4-173, A0A0P7W0C8_9TELE 182-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
S | 5-hydroxytryptamine receptor 1B | 5HT1B_HUMAN 34-390
Non-standard residues in 6g79 #3
---
EP5 — 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-
ethoxy]-1~{H}-indol-3-yl]ethylazanium
> hide #!2 models
> view
> select #3/S
1993 atoms, 2052 bonds, 3 pseudobonds, 263 residues, 2 models selected
> color (#!3 & sel) #ffca5eff
> color (#!3 & sel) #ffcb5fff
> color (#!3 & sel) #ffd470ff
> color (#!3 & sel) #ffe38cff
> color (#!3 & sel) #ffe992ff
> color (#!3 & sel) #ffed97ff
> color (#!3 & sel) #fff49fff
> color (#!3 & sel) #fffaa6ff
> color (#!3 & sel) #f3ffb7ff
> color (#!3 & sel) #e5ffbdff
> color (#!3 & sel) #d6ffbdff
> color (#!3 & sel) #cdffbbff
> color (#!3 & sel) #ccffbbff
> color (#!3 & sel) #cdffbbff
> color (#!3 & sel) #cdffbaff
> color (#!3 & sel) #beffb5ff
> color (#!3 & sel) #a7ffb2ff
> color (#!3 & sel) #a2ffb4ff
> color (#!3 & sel) #9effb6ff
> color (#!3 & sel) #9cffb9ff
> color (#!3 & sel) #99ffbcff
> color (#!3 & sel) #92ffbfff
> color (#!3 & sel) #8effc0ff
> color (#!3 & sel) #a1ffb9ff
> color (#!3 & sel) #a5ffb3ff
> color (#!3 & sel) #a5ffb0ff
> color (#!3 & sel) #a4ffadff
> color (#!3 & sel) #a3ffa3ff
> color (#!3 & sel) #a7ffa3ff
> color (#!3 & sel) #a8ffa2ff
> color (#!3 & sel) #acffa0ff
> color (#!3 & sel) #adffa0ff
> color (#!3 & sel) #b2ffa1ff
> color (#!3 & sel) #b9ff9eff
> color (#!3 & sel) #bbff9cff
> color (#!3 & sel) #bbff95ff
> color (#!3 & sel) #baff90ff
> color (#!3 & sel) #baff8eff
> color (#!3 & sel) #bbff89ff
> color (#!3 & sel) #beff80ff
> color (#!3 & sel) #c2ff7dff
> color (#!3 & sel) #c6ff7bff
> color (#!3 & sel) #ccff77ff
> color (#!3 & sel) #cfff75ff
> color (#!3 & sel) #d1ff73ff
> color (#!3 & sel) #d6ff6dff
> color (#!3 & sel) #d6ff6cff
> color (#!3 & sel) #d7ff6aff
> color (#!3 & sel) #d7ff69ff
> color (#!3 & sel) #d8ff68ff
> color (#!3 & sel) #d9ff66ff
> color (#!3 & sel) #daff65ff
> color (#!3 & sel) #dbff62ff
> color (#!3 & sel) #dbff5eff
> color (#!3 & sel) #dcff5cff
> color (#!3 & sel) #e3ff5cff
> color (#!3 & sel) #e5ff5bff
> color (#!3 & sel) #e7ff5bff
> color (#!3 & sel) #e8ff60ff
> color (#!3 & sel) #eaff64ff
> color (#!3 & sel) #eeff6cff
> color (#!3 & sel) #f0ff70ff
> color (#!3 & sel) #f1ff71ff
> color (#!3 & sel) #f3ff78ff
> color (#!3 & sel) #f4ff7cff
> color (#!3 & sel) #f4ff81ff
> color (#!3 & sel) #f5ff8aff
> color (#!3 & sel) #f7ff8fff
> color (#!3 & sel) #f7ff92ff
> color (#!3 & sel) #f8ff95ff
> color (#!3 & sel) #f8ff96ff
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> color (#!3 & sel) #f5ffa6ff
> color (#!3 & sel) #f5ffabff
> color (#!3 & sel) #f6ffafff
> color (#!3 & sel) #f7ffb2ff
> color (#!3 & sel) #f6ffb3ff
> color (#!3 & sel) #f6ffb2ff
> color (#!3 & sel) #f5ffb1ff
> color (#!3 & sel) #f3ffa8ff
> color (#!3 & sel) #f1ffa1ff
> color (#!3 & sel) #f0ff9dff
> color (#!3 & sel) #f0ff9cff
> color (#!3 & sel) #f0ff9bff
> color (#!3 & sel) #f0ff98ff
> color (#!3 & sel) #eeff91ff
> color (#!3 & sel) #edff8cff
> color (#!3 & sel) #edff8bff
> select clear
> select #3/A
1448 atoms, 1473 bonds, 2 pseudobonds, 209 residues, 2 models selected
> color (#!3 & sel) #e7ff96ff
> color (#!3 & sel) #e7ff9bff
> color (#!3 & sel) #eeffafff
> color (#!3 & sel) #faffc4ff
> color (#!3 & sel) #fffad1ff
> color (#!3 & sel) #fff0d8ff
> color (#!3 & sel) #ffd5d0ff
> color (#!3 & sel) #ffcac6ff
> color (#!3 & sel) #ffbebaff
> color (#!3 & sel) #ffb3afff
> color (#!3 & sel) #ffaeaaff
> color (#!3 & sel) #ffaba8ff
> color (#!3 & sel) #ffa9a6ff
> color (#!3 & sel) #ffa6a2ff
> color (#!3 & sel) #ff9d96ff
> color (#!3 & sel) #ff9b93ff
> color (#!3 & sel) #ff9a91ff
> color (#!3 & sel) #ff998fff
> color (#!3 & sel) #ff9a8bff
> color (#!3 & sel) #ff9b8aff
> color (#!3 & sel) #ff9b88ff
> color (#!3 & sel) #ff9b87ff
> color (#!3 & sel) #ff9c88ff
> color (#!3 & sel) #ff9c89ff
> color (#!3 & sel) #ff9f8dff
> color (#!3 & sel) #ffa08fff
> color (#!3 & sel) #ffa090ff
> color (#!3 & sel) #ffa192ff
> color (#!3 & sel) #ffa294ff
> color (#!3 & sel) #ffa394ff
> select #3/B
2270 atoms, 2315 bonds, 1 pseudobond, 333 residues, 2 models selected
> color (#!3 & sel) #fff3daff
> color (#!3 & sel) #ffede0ff
> color (#!3 & sel) #ffe9e7ff
> color (#!3 & sel) #ffeffdff
> color (#!3 & sel) #e8e1ffff
> color (#!3 & sel) #c7c9ffff
> color (#!3 & sel) #bdc3ffff
> color (#!3 & sel) #b8c0ffff
> color (#!3 & sel) #b7c0ffff
> color (#!3 & sel) #b4c0ffff
> color (#!3 & sel) #adbfffff
> color (#!3 & sel) #a0bcffff
> color (#!3 & sel) #96b9ffff
> color (#!3 & sel) #91b7ffff
> color (#!3 & sel) #87b5ffff
> color (#!3 & sel) #80b4ffff
> color (#!3 & sel) #79b3ffff
> color (#!3 & sel) #77b3ffff
> color (#!3 & sel) #77b4ffff
> color (#!3 & sel) #78b5ffff
> color (#!3 & sel) #79b7ffff
> color (#!3 & sel) #7ab7ffff
> color (#!3 & sel) #7ab8ffff
> color (#!3 & sel) #7ab7ffff
> color (#!3 & sel) #81b9ffff
> color (#!3 & sel) #8ab9ffff
> color (#!3 & sel) #8bbaffff
> color (#!3 & sel) #92bbffff
> color (#!3 & sel) #9abbffff
> color (#!3 & sel) #a1baffff
> color (#!3 & sel) #a3baffff
> color (#!3 & sel) #a5b9ffff
> color (#!3 & sel) #a6b9ffff
> color (#!3 & sel) #a6b8ffff
> color (#!3 & sel) #a5b8ffff
> color (#!3 & sel) #96b1ffff
> color (#!3 & sel) #83aeffff
> color (#!3 & sel) #74acffff
> color (#!3 & sel) #67aaffff
> color (#!3 & sel) #66aaffff
> color (#!3 & sel) #65aaffff
> color (#!3 & sel) #64aaffff
> color (#!3 & sel) #61a9ffff
> color (#!3 & sel) #62aaffff
> color (#!3 & sel) #64acffff
> color (#!3 & sel) #65adffff
> color (#!3 & sel) #66adffff
> color (#!3 & sel) #66aeffff
> color (#!3 & sel) #67aeffff
> color (#!3 & sel) #68afffff
> color (#!3 & sel) #69afffff
> color (#!3 & sel) #6ab1ffff
> color (#!3 & sel) #6ab2ffff
> color (#!3 & sel) #6bb2ffff
> color (#!3 & sel) #6bb4ffff
> color (#!3 & sel) #6db6ffff
> color (#!3 & sel) #6eb8ffff
> color (#!3 & sel) #6eb9ffff
> color (#!3 & sel) #6fbbffff
> color (#!3 & sel) #72baffff
> color (#!3 & sel) #74b9ffff
> color (#!3 & sel) #75b8ffff
> color (#!3 & sel) #76b7ffff
> select #3/G
342 atoms, 348 bonds, 56 residues, 1 model selected
> color sel #79baffff
> color sel #7eb0ffff
> color sel #80aaffff
> color sel #81a3ffff
> color sel #838effff
> color sel #838bffff
> color sel #8182ffff
> color sel #827fffff
> color sel #857dffff
> color sel #867cffff
> color sel #887affff
> color sel #8b76ffff
> color sel #8c75ffff
> color sel #8f72ffff
> color sel #9172ffff
> color sel #936fffff
> color sel #986dffff
> color sel #986cffff
> color sel #9c69ffff
> color sel #9d69ffff
> color sel #9e68ffff
> color sel #9f67ffff
> color sel #9f66ffff
> color sel #a066ffff
> color sel #a165ffff
> color sel #a264ffff
> color sel #a364ffff
> color sel #a563ffff
> color sel #a562ffff
> color sel #a563ffff
> color sel #a663ffff
> color sel #a766ffff
> color sel #a767ffff
> color sel #a869ffff
> color sel #a96affff
> color sel #aa6bffff
> color sel #aa6dffff
> color sel #ab6effff
> color sel #ab6fffff
> color sel #aa70ffff
> color sel #aa71ffff
> color sel #ab75ffff
> color sel #ab76ffff
> color sel #ad79ffff
> color sel #ad7affff
> color sel #ad7bffff
> color sel #ae7dffff
> color sel #af7fffff
> color sel #b082ffff
> color sel #b083ffff
> color sel #b287ffff
> color sel #b388ffff
> color sel #b58cffff
> select clear
> cartoon style helix width 1.0 thickness 0.2
> cartoon style helix width 1.4 thickness 0.2
> cartoon style helix width 1.3 thickness 0.2
> select ::name="EP5"
30 atoms, 33 bonds, 1 residue, 1 model selected
> color sel orange red
> color sel byhetero
> select clear
> label delete
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/S
Alignment identifier is 3/S
> select #3/S:147
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/S:147
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:351
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:351
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-
> Monash/Thesis_DL/Figures/Chapter1/mG_protein bound complex.png" width 2000
> height 1569 supersample 3 transparentBackground true
> ui tool show H-Bonds
> select #3/S:147
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
3 hydrogen bonds found
> ui tool show H-Bonds
> hbonds reveal true
1778 hydrogen bonds found
> hbonds reveal true
1778 hydrogen bonds found
> select ~sel & ##selected
6047 atoms, 6188 bonds, 658 pseudobonds, 861 residues, 3 models selected
> undo
> ui tool show H-Bonds
> hbonds makePseudobonds false relax false select true reveal true
854 hydrogen bonds found
> hbonds makePseudobonds false relax false
854 hydrogen bonds found
> hbonds makePseudobonds false relax false
854 hydrogen bonds found
> hbonds makePseudobonds false interModel false intraModel false relax false
> intraMol false intraRes false
0 hydrogen bonds found
> ui tool show H-Bonds
> help help:user/tools/hbonds.html
> delete bonds
> hbonds delete
> waters delete
Unknown command: waters delete
> hide sel & #!3 atoms
> show sel & #!3 atoms
> select clear
> delete water
Missing or invalid "atoms" argument: invalid atoms specifier
> water delete
Unknown command: water delete
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> close #3
> open 6g79
6g79 title:
Coupling specificity of heterotrimeric Go to the serotonin 5-HT1B receptor
[more info...]
Chain information for 6g79 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(o) subunit alpha | GNAO_HUMAN 4-173, A0A0P7W0C8_9TELE 182-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
S | 5-hydroxytryptamine receptor 1B | 5HT1B_HUMAN 34-390
Non-standard residues in 6g79 #3
---
EP5 — 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-
ethoxy]-1~{H}-indol-3-yl]ethylazanium
> label delete
> select #3/S
1993 atoms, 2052 bonds, 3 pseudobonds, 263 residues, 2 models selected
> color (#!3 & sel) #f9ffbdff
> color (#!3 & sel) #f6ffb7ff
> color (#!3 & sel) #f4ffb2ff
> color (#!3 & sel) #efffa3ff
> color (#!3 & sel) #eeffa3ff
> color (#!3 & sel) #eeffa1ff
> color (#!3 & sel) #ecff9dff
> color (#!3 & sel) #e8ff97ff
> color (#!3 & sel) #e0ff8cff
> color (#!3 & sel) #dcff88ff
> color (#!3 & sel) #dbff88ff
> color (#!3 & sel) #d9ff87ff
> color (#!3 & sel) #d8ff87ff
> color (#!3 & sel) #ceff89ff
> color (#!3 & sel) #cbff8dff
> color (#!3 & sel) #caff8eff
> color (#!3 & sel) #c9ff8fff
> color (#!3 & sel) #c9ff90ff
> color (#!3 & sel) #c8ff90ff
> color (#!3 & sel) #c9ff92ff
> color (#!3 & sel) #ceff92ff
> color (#!3 & sel) #d6ff93ff
> color (#!3 & sel) #eaff92ff
> color (#!3 & sel) #edff91ff
> color (#!3 & sel) #efff92ff
> color (#!3 & sel) #f0ff93ff
> color (#!3 & sel) #f1ff93ff
> color (#!3 & sel) #f3ff95ff
> color (#!3 & sel) #f4ff96ff
> color (#!3 & sel) #f6ff98ff
> color (#!3 & sel) #f6ff99ff
> color (#!3 & sel) #f3ff9fff
> color (#!3 & sel) #f2ff9fff
> color (#!3 & sel) #f3ff9bff
> color (#!3 & sel) #f5ff93ff
> color (#!3 & sel) #f8ff89ff
> color (#!3 & sel) #f8ff88ff
> color (#!3 & sel) #f8ff86ff
> color (#!3 & sel) #f8ff85ff
> color (#!3 & sel) #f8ff83ff
> color (#!3 & sel) #f8ff7fff
> select #2/A
1679 atoms, 650 pseudobonds, 217 residues, 2 models selected
> color #3 #f9ff9dff
> color #3 #f9ff9cff
> color #3 #fffb9fff
> color #3 #ffcaa5ff
> color #3 #ffbea3ff
> color #3 #ffbda3ff
> color #3 #ffbca3ff
> color #3 #ffbca0ff
> color #3 #ffbb9eff
> color #3 #ffbc98ff
> color #3 #ffbd95ff
> color #3 #ffbe93ff
> color #3 #ffbf92ff
> color #3 #ffbf91ff
> color #3 #ffbf90ff
> color #3 #ffbf8fff
> color #3 #ffbf8eff
> color #3 #ffbf8cff
> color #3 #ffbf8aff
> color #3 #ffc089ff
> select #3/S
1993 atoms, 2052 bonds, 3 pseudobonds, 263 residues, 2 models selected
> color (#!3 & sel) #ffbf79ff
> color (#!3 & sel) #ffbf7aff
> color (#!3 & sel) #ffc073ff
> color (#!3 & sel) #ffc961ff
> color (#!3 & sel) #ffcb5eff
> color (#!3 & sel) #ffcc5dff
> color (#!3 & sel) #ffcd5dff
> color (#!3 & sel) #ffd159ff
> color (#!3 & sel) #ffd257ff
> color (#!3 & sel) #ffd455ff
> color (#!3 & sel) #ffd554ff
> color (#!3 & sel) #ffdb57ff
> color (#!3 & sel) #ffe568ff
> color (#!3 & sel) #ffe878ff
> color (#!3 & sel) #ffe77eff
> color (#!3 & sel) #ffe67fff
> color (#!3 & sel) #ffe681ff
> color (#!3 & sel) #ffe682ff
> color (#!3 & sel) #ffe684ff
> color (#!3 & sel) #ffe784ff
> color (#!3 & sel) #ffe786ff
> color (#!3 & sel) #ffe887ff
> color (#!3 & sel) #ffe989ff
> select #3/A
1448 atoms, 1473 bonds, 2 pseudobonds, 209 residues, 2 models selected
> color (#!3 & sel) #ffe97eff
> color (#!3 & sel) #ffe781ff
> color (#!3 & sel) #ffe484ff
> color (#!3 & sel) #ffd791ff
> color (#!3 & sel) #ffd493ff
> color (#!3 & sel) #ffd394ff
> color (#!3 & sel) #ffd197ff
> color (#!3 & sel) #ffcf99ff
> color (#!3 & sel) #ffce9aff
> color (#!3 & sel) #ffcc9bff
> color (#!3 & sel) #ffca9cff
> color (#!3 & sel) #ffc697ff
> color (#!3 & sel) #ffb67eff
> color (#!3 & sel) #ffae73ff
> color (#!3 & sel) #ffad71ff
> color (#!3 & sel) #ffaa6dff
> color (#!3 & sel) #ffa768ff
> color (#!3 & sel) #ffa464ff
> color (#!3 & sel) #ffa362ff
> color (#!3 & sel) #ffa262ff
> color (#!3 & sel) #ffa15fff
> color (#!3 & sel) #ff9d5aff
> color (#!3 & sel) #ff9c59ff
> color (#!3 & sel) #ff9a51ff
> color (#!3 & sel) #ff994dff
> color (#!3 & sel) #ff994cff
> color (#!3 & sel) #ff984aff
> color (#!3 & sel) #ff974aff
> color (#!3 & sel) #ff9747ff
> color (#!3 & sel) #ff9646ff
> color (#!3 & sel) #ff9645ff
> color (#!3 & sel) #ff9545ff
> color (#!3 & sel) #ff9344ff
> color (#!3 & sel) #ff9145ff
> color (#!3 & sel) #ff8d49ff
> color (#!3 & sel) #ff8b4dff
> color (#!3 & sel) #ff8a4eff
> color (#!3 & sel) #ff894fff
> color (#!3 & sel) #ff8a50ff
> color (#!3 & sel) #ff8d54ff
> color (#!3 & sel) #ff8e54ff
> color (#!3 & sel) #ff8e53ff
> color (#!3 & sel) #ff8c4cff
> color (#!3 & sel) #ff8a46ff
> select #3/S
1993 atoms, 2052 bonds, 3 pseudobonds, 263 residues, 2 models selected
> color (#!3 & sel) #ff914eff
> color (#!3 & sel) #ff974fff
> color (#!3 & sel) #ffa453ff
> color (#!3 & sel) #ffa855ff
> color (#!3 & sel) #ffa856ff
> color (#!3 & sel) #ffad57ff
> color (#!3 & sel) #ffb258ff
> color (#!3 & sel) #ffb657ff
> color (#!3 & sel) #ffb956ff
> color (#!3 & sel) #ffbb55ff
> color (#!3 & sel) #ffbd55ff
> color (#!3 & sel) #ffbe53ff
> color (#!3 & sel) #ffc052ff
> color (#!3 & sel) #ffc150ff
> color (#!3 & sel) #ffc64aff
> color (#!3 & sel) #ffc74aff
> color (#!3 & sel) #ffc849ff
> color (#!3 & sel) #ffca4aff
> color (#!3 & sel) #ffcc4bff
> color (#!3 & sel) #ffcf4cff
> color (#!3 & sel) #ffd34cff
> color (#!3 & sel) #ffd54bff
> color (#!3 & sel) #ffdb48ff
> color (#!3 & sel) #ffdd45ff
> color (#!3 & sel) #ffdf42ff
> color (#!3 & sel) #ffe140ff
> color (#!3 & sel) #ffe33eff
> color (#!3 & sel) #ffe541ff
> color (#!3 & sel) #ffe948ff
> color (#!3 & sel) #ffea51ff
> color (#!3 & sel) #ffe957ff
> color (#!3 & sel) #ffe959ff
> color (#!3 & sel) #ffea5cff
> color (#!3 & sel) #ffee65ff
> color (#!3 & sel) #fff06aff
> color (#!3 & sel) #fff273ff
> color (#!3 & sel) #fff279ff
> color (#!3 & sel) #fff27dff
> color (#!3 & sel) #fff27fff
> color (#!3 & sel) #fff387ff
> color (#!3 & sel) #fff38aff
> color (#!3 & sel) #fff48eff
> color (#!3 & sel) #fff48fff
> color (#!3 & sel) #fff592ff
> color (#!3 & sel) #fff593ff
> color (#!3 & sel) #fff698ff
> color (#!3 & sel) #fff69aff
> color (#!3 & sel) #fff79cff
> color (#!3 & sel) #fffaa2ff
> color (#!3 & sel) #fffe9cff
> color (#!3 & sel) #ffff9cff
> color (#!3 & sel) #feff9bff
> color (#!3 & sel) #fdff99ff
> color (#!3 & sel) #fcff98ff
> color (#!3 & sel) #fcff97ff
> color (#!3 & sel) #fbff97ff
> color (#!3 & sel) #fcff98ff
> color (#!3 & sel) #faff95ff
> color (#!3 & sel) #f8ff8dff
> color (#!3 & sel) #f8ff8bff
> color (#!3 & sel) #f7ff89ff
> color (#!3 & sel) #f7ff8aff
> color (#!3 & sel) #ebffafff
> color (#!3 & sel) #e8ffbcff
> color (#!3 & sel) #e1f7ffff
> color (#!3 & sel) #9fafffff
> color (#!3 & sel) #9bacffff
> color (#!3 & sel) #9aacffff
> color (#!3 & sel) #98b4ffff
> color (#!3 & sel) #95bbffff
> color (#!3 & sel) #95c2ffff
> color (#!3 & sel) #96c8ffff
> color (#!3 & sel) #96d1ffff
> color (#!3 & sel) #95d5ffff
> color (#!3 & sel) #94d9ffff
> color (#!3 & sel) #94dbffff
> color (#!3 & sel) #94ddffff
> color (#!3 & sel) #95e2ffff
> color (#!3 & sel) #95e4ffff
> color (#!3 & sel) #95e5ffff
> color (#!3 & sel) #96e7ffff
> color (#!3 & sel) #96e8ffff
> color (#!3 & sel) #9eebffff
> color (#!3 & sel) #a5edffff
> color (#!3 & sel) #afeeffff
> color (#!3 & sel) #b6efffff
> color (#!3 & sel) #b9efffff
> color (#!3 & sel) #beeeffff
> color (#!3 & sel) #c2ecffff
> color (#!3 & sel) #c6ecffff
> color (#!3 & sel) #cdecffff
> color (#!3 & sel) #cdebffff
> color (#!3 & sel) #cbe9ffff
> color (#!3 & sel) #c9e8ffff
> color (#!3 & sel) #c6e5ffff
> color (#!3 & sel) #c5e5ffff
> color (#!3 & sel) #bee3ffff
> color (#!3 & sel) #b9e2ffff
> color (#!3 & sel) #b3e0ffff
> color (#!3 & sel) #afdfffff
> color (#!3 & sel) #aedfffff
> color (#!3 & sel) #addeffff
> color (#!3 & sel) #acdfffff
> color (#!3 & sel) #a6e1ffff
> color (#!3 & sel) #a2e1ffff
> color (#!3 & sel) #a0e0ffff
> color (#!3 & sel) #a0e2ffff
> color (#!3 & sel) #9fe3ffff
> color (#!3 & sel) #9fe4ffff
> color (#!3 & sel) #9ee8ffff
> color (#!3 & sel) #9ceaffff
> color (#!3 & sel) #9cebffff
> color (#!3 & sel) #97e6ffff
> color (#!3 & sel) #90e1ffff
> color (#!3 & sel) #86d8ffff
> color (#!3 & sel) #83d5ffff
> color (#!3 & sel) #7ecfffff
> color (#!3 & sel) #7ccdffff
> color (#!3 & sel) #7bccffff
> color (#!3 & sel) #7acbffff
> color (#!3 & sel) #78c9ffff
> color (#!3 & sel) #77c9ffff
> color (#!3 & sel) #76c9ffff
> color (#!3 & sel) #75c8ffff
> color (#!3 & sel) #70c7ffff
> color (#!3 & sel) #73c7ffff
> color (#!3 & sel) #77c8ffff
> color (#!3 & sel) #78c8ffff
> color (#!3 & sel) #79c8ffff
> color (#!3 & sel) #7cc7ffff
> color (#!3 & sel) #7dc8ffff
> color (#!3 & sel) #7dc7ffff
> color (#!3 & sel) #7ac5ffff
> select #3/B
2270 atoms, 2315 bonds, 1 pseudobond, 333 residues, 2 models selected
> color (#!3 & sel) #72d7ffff
> color (#!3 & sel) #74d7ffff
> color (#!3 & sel) #77d8ffff
> color (#!3 & sel) #8ad6ffff
> color (#!3 & sel) #a2d6ffff
> color (#!3 & sel) #b2d6ffff
> color (#!3 & sel) #b5d6ffff
> color (#!3 & sel) #b8d7ffff
> color (#!3 & sel) #bdd9ffff
> color (#!3 & sel) #cbdfffff
> color (#!3 & sel) #d3e3ffff
> color (#!3 & sel) #d4e3ffff
> color (#!3 & sel) #ced5ffff
> color (#!3 & sel) #cbcfffff
> color (#!3 & sel) #c5c4ffff
> color (#!3 & sel) #c2beffff
> color (#!3 & sel) #bfbaffff
> color (#!3 & sel) #bfb9ffff
> color (#!3 & sel) #beb6ffff
> color (#!3 & sel) #bbb1ffff
> color (#!3 & sel) #b8aaffff
> color (#!3 & sel) #b6a7ffff
> color (#!3 & sel) #b3a1ffff
> color (#!3 & sel) #b19dffff
> color (#!3 & sel) #af99ffff
> color (#!3 & sel) #aa97ffff
> color (#!3 & sel) #a295ffff
> color (#!3 & sel) #a294ffff
> color (#!3 & sel) #9f94ffff
> color (#!3 & sel) #9497ffff
> color (#!3 & sel) #979dffff
> color (#!3 & sel) #9aa2ffff
> color (#!3 & sel) #9ea6ffff
> color (#!3 & sel) #a2abffff
> color (#!3 & sel) #a7aeffff
> color (#!3 & sel) #b6b4ffff
> color (#!3 & sel) #bbb6ffff
> color (#!3 & sel) #cabdffff
> color (#!3 & sel) #d5c1ffff
> color (#!3 & sel) #dac3ffff
> color (#!3 & sel) #dec4ffff
> color (#!3 & sel) #ebc7ffff
> color (#!3 & sel) #f1c7ffff
> color (#!3 & sel) #f5c8ffff
> color (#!3 & sel) #f7c8ffff
> color (#!3 & sel) #fac6ffff
> color (#!3 & sel) #ffc3ffff
> color (#!3 & sel) #ffbff8ff
> color (#!3 & sel) #ffbef7ff
> color (#!3 & sel) #ffbcf2ff
> color (#!3 & sel) #ffbaefff
> color (#!3 & sel) #ffb7ebff
> color (#!3 & sel) #ffb7eaff
> color (#!3 & sel) #ffb5e7ff
> color (#!3 & sel) #ffb3e5ff
> color (#!3 & sel) #ffb2e4ff
> color (#!3 & sel) #ffb2e2ff
> color (#!3 & sel) #ffb0e0ff
> color (#!3 & sel) #ffb0dfff
> color (#!3 & sel) #ffb1dfff
> color (#!3 & sel) #ffb3deff
> color (#!3 & sel) #ffb9ddff
> color (#!3 & sel) #ffbbddff
> color (#!3 & sel) #ffbddcff
> color (#!3 & sel) #ffc1dbff
> color (#!3 & sel) #ffc3d9ff
> color (#!3 & sel) #ffc4d9ff
> color (#!3 & sel) #ffc5d8ff
> color (#!3 & sel) #ffc9daff
> color (#!3 & sel) #ffccdcff
> color (#!3 & sel) #ffd1dfff
> color (#!3 & sel) #ffd3e0ff
> color (#!3 & sel) #ffd8d8ff
> color (#!3 & sel) #ffdbd8ff
> color (#!3 & sel) #ffded9ff
> color (#!3 & sel) #ffe3d8ff
> color (#!3 & sel) #ffead5ff
> color (#!3 & sel) #ffecd3ff
> color (#!3 & sel) #ffeecfff
> color (#!3 & sel) #ffefccff
> color (#!3 & sel) #fff0cbff
> color (#!3 & sel) #fff0caff
> color (#!3 & sel) #fff0cbff
> select #3/G
342 atoms, 348 bonds, 56 residues, 1 model selected
> color sel #f2ffdfff
> color sel #f3ffe3ff
> color sel #f6ffeaff
> color sel #fcfffdff
> color sel #dbceffff
> color sel #c5acffff
> color sel #bda1ffff
> color sel #b99bffff
> color sel #b290ffff
> color sel #b18dffff
> color sel #b08dffff
> color sel #b08bffff
> color sel #af89ffff
> color sel #af88ffff
> color sel #af85ffff
> color sel #ae82ffff
> color sel #af80ffff
> color sel #af7fffff
> color sel #ae7cffff
> color sel #ae7affff
> color sel #ad78ffff
> color sel #ad77ffff
> color sel #ac76ffff
> color sel #ac75ffff
> color sel #a872ffff
> color sel #a772ffff
> color sel #a470ffff
> color sel #9f6effff
> color sel #9e6effff
> color sel #9e6dffff
> color sel #9e6effff
> color sel #9f70ffff
> color sel #a173ffff
> color sel #a379ffff
> color sel #a580ffff
> color sel #a783ffff
> color sel #a987ffff
> color sel #ac8dffff
> color sel #ad8fffff
> color sel #ae90ffff
> color sel #af92ffff
> color sel #b093ffff
> color sel #b094ffff
> color sel #b195ffff
> color sel #b296ffff
> color sel #b297ffff
> color sel #b296ffff
> color sel #b195ffff
> color sel #b194ffff
> color sel #af8fffff
> color sel #ad8affff
> color sel #ad89ffff
> color sel #ac88ffff
> color sel #ab85ffff
> color sel #a880ffff
> color sel #a87fffff
> color sel #a87effff
> color sel #a87dffff
> color sel #a77dffff
> color sel #a77cffff
> color sel #a579ffff
> color sel #a477ffff
> cartoon style helix width 1.3 thickness 0.2
> ui tool show "Show Sequence Viewer"
> sequence chain #3/S
Alignment identifier is 3/S
> select #3/S:161
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/S:161
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/S:147
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/S:147
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:351
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:351
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select ::name="EP5"
30 atoms, 33 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select ::name="EP5"
30 atoms, 33 bonds, 1 residue, 1 model selected
> color sel forest green
> color sel byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-
> Monash/Thesis_DL/Figures/Chapter1/mG_protein bound complex2.png" width 2000
> height 1569 supersample 3 transparentBackground true
> save "/Users/dongju/Desktop/Research projects-
> Monash/Thesis_DL/Figures/Chapter1/mG_protein bound complex2_focused.png"
> width 1500 height 1177 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-7.0.23
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
OS Loader Version: 583~2210
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 26 days, 22 hours, 42 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
This is the common Mac AMD graphics driver crash. Nothing we can do about Apple's unstable AMD graphics drivers.