The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403171404 (2024-03-17 14:04:18 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002bef83000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002bdf77000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002bcf6b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002bbf5f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002baf53000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b9f47000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b8f3b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b7f2f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b6f23000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b5f17000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b4f0b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b3eff000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002b2ef3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001dd989c40 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/util.py", line 73 in copyMolecule
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/motion.py", line 81 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/motion.py", line 17 in compute_morph
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/morph/morph.py", line 84 in morph
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 54)
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{
"uptime" : 440000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 48516,
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"build" : "23D60",
"releaseType" : "User"
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"captureTime" : "2024-03-19 07:51:55.9214 -0500",
"codeSigningMonitor" : 1,
"incident" : "10012514-5395-4B88-80D6-D621D47AA90E",
"pid" : 60528,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-03-19 07:01:15.2671 -0500",
"procStartAbsTime" : 10574953326663,
"procExitAbsTime" : 10647927131305,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D3179976-8925-5323-AAEE-8F872221340E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
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"crashReporterKey" : "786FE3D2-07D3-926F-F7A1-D57899368D3D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 3564,
"sleepWakeUUID" : "4AC58CEF-E4ED-408B-94DC-911970CCAED2",
"sip" : "enabled",
"vmRegionInfo" : "0x175e20c is not in any region. Bytes before following region: 4304362996\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102054000-102058000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000175e20c","rawCodes":[1,24502796],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000175e20c"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":60528},
"vmregioninfo" : "0x175e20c is not in any region. Bytes before following region: 4304362996\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102054000-102058000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8.dev202403171404 (2024-03-17)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd "/Users/marcel/Library/CloudStorage/Box-Box/Goldschen-Ohm Lab/GABAAR"
Current working directory is: /Users/marcel/Library/CloudStorage/Box-
Box/Goldschen-Ohm Lab/GABAAR
> runscript GABAAR.cxc
> close
> log clear
> set bgColor gainsboro
> camera ortho
> open 6x3s id 1
Summary of feedback from opening 6x3s fetched from pdb
---
notes | Fetching compressed mmCIF 6x3s from http://files.rcsb.org/download/6x3s.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
Fetching CCD J94 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/J94/J94.cif
6x3s title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline
methbromide [more info...]
Chain information for 6x3s #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid type A receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3s #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
J94 —
(5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> name human_a1b2g2_bicuculline_Hibbs #1
> open 6x3z id 2
Summary of feedback from opening 6x3z fetched from pdb
---
note | Fetching compressed mmCIF 6x3z from http://files.rcsb.org/download/6x3z.cif
6x3z title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA [more
info...]
Chain information for 6x3z #2
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3z #2
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> name human_a1b2g2_GABA_Hibbs #2
> name human human_a1b2g2_bicuculline_Hibbs | human_a1b2g2_GABA_Hibbs
> name mouse ~human
> name align_ref human_a1b2g2_bicuculline_Hibbs & /A-E & (helix | strand)
> align human_a1b2g2_GABA_Hibbs & /A-E & (helix | strand) toAtoms align_ref move structures matchNumbering true matchChainIds true
Pairing dropped 493 atoms and 512 reference atoms
RMSD between 8995 atom pairs is 1.705 angstroms
> cofr align_ref
> name a1 /B,D
> name b2 /A,C
> name g2 /E
> name fab protein & ~/A-E
> name glycan :BMA,MAN,NAG
> name lipid :Q3G,POV,PTY
> name GABA :ABU
> name bicuculline :J94
> name PTX :RI5
> name diazepam :DZP
> name diazepam_ECD /D:DZP
> name diazepam_TMD diazepam & ~diazepam_ECD
> name flumazenil :FYP
> name zolpidem :R5R
> name DMCM :R63
> name etomidate :V8D
> name propofol :PFL
> name phenobarbital :UQA
> name pregnenolone_sulfate :A8W
> name allopregnanolone :Y4B
> name dehydroepiandrosterone_sulfate :ZWY
> name ECD (a1 & :1-222) | (b2 & :1-217) | (g2 & :1-232)
> name TMD (a1 & :223-347) | (b2 & :218-340) | (g2 & :233-357)
> name M2 (a1 & ((human & :251-277) | (mouse & :250-276))) | (b2 & :246-272) | (g2 & :261-286)
> name M23 (a1 & ((human & :277-284) | (mouse & :276-283))) | (b2 & :272-279) | (g2 & :286-294)
> name L9gate (a1 & ((human & :264) | (mouse & :263))) | (b2 & :259) | (g2 & :274)
> lighting soft
> lighting shadows true
> graphics silhouettes true
> set silhouetteWidth 1.5
> lighting depthCue true
> ~display protein
> ribbon
> style all stick
Changed 34772 atom styles
> color a1 & protein rgb(75,88,26)
> color modify a1 & protein lightness 75
> color a1 & protein rgb(245,255,182)
> color b2 & protein light steel blue
> color g2 & protein bisque
> color fab light gray
> color ligand cyan
> color glycan light gray
> color lipid peru
> color ~protein byhetero
> display L9gate
> view zalign ECD inFrontOf TMD
> view all
> turn z 240
> zoom 2.25
> view name topdown
> turn x -180
> view name bottomup
> turn x 90
> view all
> zoom 1.82
> view name side_bag
> ~ribbon fab
> ~display glycan
> ui tool show "Side View"
> hbonds M23 restrict both interModel false relax true distSlop 0.4 angleSlop
> 45 reveal true radius 0.2 color cyan
19 hydrogen bonds found
> hide #!2 models
> display M23 sticks
> show M23 sticks
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display M23
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A #1/C #2/A #2/C
Alignment identifier is 1
> color M23 by heteroatom
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color M23 byhetero
> select #1/A,C:226 #2/A,C:226
48 atoms, 48 bonds, 4 residues, 2 models selected
> select #1/A,C:226-270 #2/A,C:226-270
1428 atoms, 1460 bonds, 180 residues, 2 models selected
Gamma-aminobutyric Acid Receptor Subunit Beta-2 [ID: 1] region 4 chains
[226-270] RMSD: 0.936
> select #1/A,C:8-21,84-90,139-143,218-242,246-272,279-306,309-339
> #2/A,C:8-21,84-90,139-143,218-242,246-272,279-306,309-339
4552 atoms, 4652 bonds, 548 residues, 2 models selected
> select #1/A,C:218 #2/A,C:218
32 atoms, 28 bonds, 4 residues, 2 models selected
> select #1/A,C:218-223 #2/A,C:218-223
204 atoms, 208 bonds, 24 residues, 2 models selected
Gamma-aminobutyric Acid Receptor Subunit Beta-2 [ID: 1] region 4 chains
[218-223] RMSD: 0.995
> select #1/A,C:8-21,84-90,139-143,218-242,246-272,279-306,309-339
> #2/A,C:8-21,84-90,139-143,218-242,246-272,279-306,309-339
4552 atoms, 4652 bonds, 548 residues, 2 models selected
> select #1/A,C:245-246 #2/A,C:245-246
52 atoms, 48 bonds, 8 residues, 2 models selected
> select #1/A,C:246-272 #2/A,C:246-272
792 atoms, 792 bonds, 108 residues, 2 models selected
Gamma-aminobutyric Acid Receptor Subunit Beta-2 [ID: 1] region 4 chains
[246-272] RMSD: 1.547
> display sel
> color sel byhetero
> select #1/A,C:279 #2/A,C:279
36 atoms, 32 bonds, 4 residues, 2 models selected
> select #1/A,C:279-306 #2/A,C:279-306
928 atoms, 952 bonds, 112 residues, 2 models selected
Gamma-aminobutyric Acid Receptor Subunit Beta-2 [ID: 1] region 4 chains
[279-306] RMSD: 1.178
> display sel
> color sel byhetero
> ui mousemode right select
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/B #1/D #2/B #2/D
Alignment identifier is 2
> select #1/B,D:251 #2/B,D:251
24 atoms, 20 bonds, 4 residues, 2 models selected
> select #1/B,D:251-277 #2/B,D:251-277
784 atoms, 788 bonds, 108 residues, 2 models selected
Gamma-aminobutyric Acid Receptor Subunit Alpha-1 [ID: 2] region 4 chains
[251-277] RMSD: 1.326
> display sel
> color sel byhetero
> select #1/B,D:284 #2/B,D:284
28 atoms, 24 bonds, 1 pseudobond, 4 residues, 3 models selected
> select #1/B,D:284-311 #2/B,D:284-311
916 atoms, 948 bonds, 1 pseudobond, 112 residues, 3 models selected
Gamma-aminobutyric Acid Receptor Subunit Alpha-1 [ID: 2] region 4 chains
[284-311] RMSD: 1.508
> display sel
> color sel byhetero
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/E #2/E
Alignment identifier is 3
> select #1/E:261 #2/E:261
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/E:261-286 #2/E:261-286
372 atoms, 372 bonds, 52 residues, 2 models selected
Gamma-aminobutyric Acid Type A Receptor Subunit Gamma-2 [ID: 3] region 2
chains [298-323] RMSD: 1.493
> display sel
> color sel byhetero
> select #1/E:26-35,99-106,234-257,261-286,294-357
> #2/E:26-35,99-106,234-257,261-286,294-357
2100 atoms, 2150 bonds, 264 residues, 2 models selected
> select #1/E:294 #2/E:294
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/E:294 #2/E:294
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/E:294-335 #2/E:294-335
658 atoms, 676 bonds, 84 residues, 2 models selected
Gamma-aminobutyric Acid Type A Receptor Subunit Gamma-2 [ID: 3] region 2
chains [331-372] RMSD: 1.726
> select #1/E:294 #2/E:294
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/E:294-324 #2/E:294-324
496 atoms, 510 bonds, 62 residues, 2 models selected
Gamma-aminobutyric Acid Type A Receptor Subunit Gamma-2 [ID: 3] region 2
chains [331-361] RMSD: 1.415
> select #1/E:294 #2/E:294
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/E:294-322 #2/E:294-322
466 atoms, 480 bonds, 58 residues, 2 models selected
Gamma-aminobutyric Acid Type A Receptor Subunit Gamma-2 [ID: 3] region 2
chains [331-359] RMSD: 1.379
> select #1/E:294 #2/E:294
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/E:294-323 #2/E:294-323
478 atoms, 492 bonds, 60 residues, 2 models selected
Gamma-aminobutyric Acid Type A Receptor Subunit Gamma-2 [ID: 3] region 2
chains [331-360] RMSD: 1.397
> display sel
> color sel byhetero
> select clear
> display TMD
> color TMD byhetero
> show #!2 models
> hide #!1 models
> display
> runscript GABAAR.cxc
> close
> log clear
> set bgColor gainsboro
> camera ortho
> open 6x3s id 1
6x3s title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with bicuculline
methbromide [more info...]
Chain information for 6x3s #1
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid type A receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3s #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
J94 —
(5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> name human_a1b2g2_bicuculline_Hibbs #1
> open 6x3z id 2
6x3z title:
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA [more
info...]
Chain information for 6x3z #2
---
Chain | Description | UniProt
A C | Gamma-aminobutyric acid receptor subunit beta-2 | GBRB2_HUMAN 1-307 316-341
B D | Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_HUMAN 1-312 320-358
E | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN 3-322
I L | Kappa Fab Light Chain |
J K | IgG2b Fab Heavy Chain |
Non-standard residues in 6x3z #2
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> name human_a1b2g2_GABA_Hibbs #2
> name human human_a1b2g2_bicuculline_Hibbs | human_a1b2g2_GABA_Hibbs
> name mouse ~human
> name align_ref human_a1b2g2_bicuculline_Hibbs & /A-E & (helix | strand)
> align human_a1b2g2_GABA_Hibbs & /A-E & (helix | strand) toAtoms align_ref move structures matchNumbering true matchChainIds true
Pairing dropped 493 atoms and 512 reference atoms
RMSD between 8995 atom pairs is 1.705 angstroms
> cofr align_ref
> name a1 /B,D
> name b2 /A,C
> name g2 /E
> name fab protein & ~/A-E
> name glycan :BMA,MAN,NAG
> name lipid :Q3G,POV,PTY
> name GABA :ABU
> name bicuculline :J94
> name PTX :RI5
> name diazepam :DZP
> name diazepam_ECD /D:DZP
> name diazepam_TMD diazepam & ~diazepam_ECD
> name flumazenil :FYP
> name zolpidem :R5R
> name DMCM :R63
> name etomidate :V8D
> name propofol :PFL
> name phenobarbital :UQA
> name pregnenolone_sulfate :A8W
> name allopregnanolone :Y4B
> name dehydroepiandrosterone_sulfate :ZWY
> name ECD (a1 & :1-222) | (b2 & :1-217) | (g2 & :1-232)
> name TMD (a1 & :223-347) | (b2 & :218-340) | (g2 & :233-357)
> name M2 (a1 & ((human & :251-277) | (mouse & :250-276))) | (b2 & :246-272) | (g2 & :261-286)
> name M23 (a1 & ((human & :277-284) | (mouse & :276-283))) | (b2 & :272-279) | (g2 & :286-294)
> name L9gate (a1 & ((human & :264) | (mouse & :263))) | (b2 & :259) | (g2 & :274)
> lighting soft
> lighting shadows true
> graphics silhouettes true
> set silhouetteWidth 1.5
> lighting depthCue true
> ~display protein
> ribbon
> style all stick
Changed 34772 atom styles
> color a1 & protein rgb(75,88,26)
> color modify a1 & protein lightness 75
> color a1 & protein rgb(245,255,182)
> color b2 & protein light steel blue
> color g2 & protein bisque
> color fab light gray
> color ligand cyan
> color glycan light gray
> color lipid peru
> color ~protein byhetero
> display L9gate
> view zalign ECD inFrontOf TMD
> view all
> turn z 240
> zoom 2.25
> view name topdown
> turn x -180
> view name bottomup
> turn x 90
> view all
> zoom 1.82
> view name side_bag
> display M23
> color M23 byhetero
> display M23 sticks
> show M23 sticks
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2 models
> select #1/K:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> select up
914 atoms, 936 bonds, 117 residues, 1 model selected
> select #1/L:86
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/K:10
21 atoms, 20 bonds, 2 residues, 1 model selected
> select add #1/I:62
32 atoms, 31 bonds, 3 residues, 1 model selected
> select add #1/J:4
40 atoms, 38 bonds, 4 residues, 1 model selected
> select up
129 atoms, 128 bonds, 16 residues, 1 model selected
> select up
3434 atoms, 3516 bonds, 444 residues, 1 model selected
> ~ribbon
> ribbon
> ~ribbon sel
> ~display glycan
> display protein
> ~display sel
> color protein byhetero
> hbonds M23 restrict both interModel false relax true distSlop 0.4 angleSlop
> 45 reveal true radius 0.2 color cyan
19 hydrogen bonds found
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> morph #1,2 frames 25 play false
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403171404 (2024-03-17)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MK1A3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 23 days, 19 hours, 21 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG ULTRAWIDE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
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: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403171404
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.2
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.8
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.2
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.8.2
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.1.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.42.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
I can reproduce the crash with the commands in this log. I am attaching the corresponding .cxc file.