id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14783	Crash in python_instances_of_class while computing morph	chimerax-bug-report@…	Eric Pettersen	"{{{
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)


{""app_name"":""ChimeraX"",""timestamp"":""2024-03-19 07:52:03.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.3.1 (23D60)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""10012514-5395-4B88-80D6-D621D47AA90E""}
{
  ""uptime"" : 440000,
  ""procRole"" : ""Foreground"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,2"",
  ""coalitionID"" : 48516,
  ""osVersion"" : {
    ""train"" : ""macOS 14.3.1"",
    ""build"" : ""23D60"",
    ""releaseType"" : ""User""
  },
  ""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,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""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"",
  ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0},
  ""faultingThread"" : 0,
  ""threads"" : [{""threadState"":{""x"":[{""value"":0},{""value"":0},{""value"":1},{""value"":4832131736},{""value"":99},{""value"":115},{""value"":0},{""value"":0},{""value"":16465467754113743462},{""value"":16465467751369123366},{""value"":14757395258967641293},{""value"":4294967286},{""value"":4832131666},{""value"":0},{""value"":53},{""value"":4294967280},{""value"":328},{""value"":8164274936},{""value"":0},{""value"":11},{""value"":8012733504,""symbolLocation"":0,""symbol"":""_main_thread""},{""value"":259},{""value"":8012733728,""symbolLocation"":224,""symbol"":""_main_thread""},{""value"":1},{""value"":4351952432,""symbolLocation"":0,""symbol"":""faulthandler_handlers""},{""value"":0},{""value"":1},{""value"":1},{""value"":6137996976}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6560636096},""cpsr"":{""value"":1073745920},""fp"":{""value"":4832131808},""sp"":{""value"":4832131776},""esr"":{""value"":1442840704,""description"":"" Address size 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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

}}}
"	defect	closed	normal		Core		fixed		Tom Goddard Tristan Croll Ching-Fang.Chang@…				all	ChimeraX