id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14953	Crash in garbage collection	yakonfire@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000034cfa7000 (most recent call first):
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000348e1f000 (most recent call first):
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000034516f000 (most recent call first):
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001ff60fac0 (most recent call first):
  Garbage-collecting
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 60 in upairs
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 68 in update
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 19 in __init__
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 255 in _push_ast
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 494 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 464 in _atom_list_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 464 in _atom_list_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 441 in _atom_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 390 in block5
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 771 in _closure
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 392 in _residue_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 359 in block7
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 361 in _chain_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 323 in block0
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 325 in _model_parts_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 200 in _model_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 157 in block0
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 159 in _model_list_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 136 in _as_term_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 89 in _atom_specifier_
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 206 in parse
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 192 in _parse_unquoted
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 121 in parse
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py"", line 180 in defattr
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 81 in add_standard_charges
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 34 in add_charges
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 110 in assign_charges
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3468 in __call__
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2929 in run
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py"", line 184 in _run_commands
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py"", line 61 in run_command_script
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py"", line 51 in runscript
  File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run
  File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
  File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, lxml._elementpath, lxml.etree, 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, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 59)


{""app_name"":""ChimeraX"",""timestamp"":""2024-04-11 00:15:22.00 -0600"",""app_version"":""1.7.1"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.4.1 (23E224)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""44BAF6B2-4300-4BAE-887C-090223228EB6""}
{
  ""uptime"" : 250000,
  ""procRole"" : ""Foreground"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,2"",
  ""coalitionID"" : 8844,
  ""osVersion"" : {
    ""train"" : ""macOS 14.4.1"",
    ""build"" : ""23E224"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2024-04-11 00:15:21.5027 -0600"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""44BAF6B2-4300-4BAE-887C-090223228EB6"",
  ""pid"" : 34247,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2024-04-11 00:00:02.0834 -0600"",
  ""procStartAbsTime"" : 6208282033972,
  ""procExitAbsTime"" : 6230347112478,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.1"",""CFBundleVersion"":""1.7.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""54EDB63B-59DA-5473-BF40-1A458E1F4283"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""3FE89ED7-3137-4E81-0724-502C8964939F"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""},
  ""wakeTime"" : 3494,
  ""sleepWakeUUID"" : ""1E2D91F6-0AFE-439C-9DD3-DDA48B79E181"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0xa9 is not in any region.  Bytes before following region: 4308942679\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100d54000-100d58000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"",
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===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc

> alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode ""/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4""

> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae
> #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB136

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB136/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
1 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB136/AB136_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB136/AB136_contacts_hbonds_rot.mp4  
  
Changed 6523 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB136/AB136_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB136/AB136_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -16.97, mean
-2.32, maximum 9.03  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.09, mean
-1.65, maximum 12.64  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB136/AB136_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB136/AB136_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -30.77, mean
-5.236, maximum 22.37  
Map values for surface ""best_model.pdb_B SES surface"": minimum -28.15, mean
-5.266, maximum 23.03  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB136/AB136_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB136/AB136_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB137

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB137/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
0 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB137/AB137_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB137/AB137_contacts_hbonds_rot.mp4  
  
Changed 6741 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB137/AB137_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB137/AB137_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -15.62, mean
-2.71, maximum 9.19  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -19.64, mean
-0.14, maximum 13.07  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB137/AB137_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB137/AB137_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -27.55, mean
-5.384, maximum 22.14  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.32, mean
-3.383, maximum 23.33  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB137/AB137_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB137/AB137_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB138

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB138/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
12 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB138/AB138_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB138/AB138_contacts_hbonds_rot.mp4  
  
Changed 6788 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB138/AB138_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB138/AB138_sphere_rot.mp4  
  
Changed 0 atom styles  
Exception ignored in tp_clear of:   
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py"", line 157, in custom_attrs  
for attr_name, attr_info in
self.__class__._attr_registration.reg_attr_info.items():  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: NoneType takes no arguments  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.65, mean
-2.95, maximum 10.76  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -18.90, mean
-0.79, maximum 16.35  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB138/AB138_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB138/AB138_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -35.01, mean
-5.444, maximum 23.3  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.25, mean
-6.133, maximum 24.79  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB138/AB138_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB138/AB138_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB140

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB140/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
3 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB140/AB140_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB140/AB140_contacts_hbonds_rot.mp4  
  
Changed 7842 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB140/AB140_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB140/AB140_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.72, mean
-2.33, maximum 9.48  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -18.03, mean
0.50, maximum 15.78  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB140/AB140_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB140/AB140_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -26.81, mean
-5.245, maximum 22.19  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.58, mean
-2.901, maximum 23.62  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB140/AB140_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB140/AB140_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB141

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB141/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
1 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB141/AB141_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB141/AB141_contacts_hbonds_rot.mp4  
  
Changed 8427 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB141/AB141_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB141/AB141_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -15.18, mean
-2.35, maximum 8.58  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.51, mean
-0.00, maximum 14.60  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB141/AB141_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB141/AB141_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -27.89, mean
-5.234, maximum 23.79  
Map values for surface ""best_model.pdb_B SES surface"": minimum -28.43, mean
-1.69, maximum 25.57  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB141/AB141_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB141/AB141_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB144

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB144/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
11 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB144/AB144_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB144/AB144_contacts_hbonds_rot.mp4  
  
Changed 8852 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB144/AB144_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB144/AB144_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -13.29, mean
-2.57, maximum 9.33  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -45.20, mean
-3.31, maximum 14.22  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB144/AB144_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB144/AB144_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -29.59, mean
-5.275, maximum 22.97  
Map values for surface ""best_model.pdb_B SES surface"": minimum -30.51, mean
-5.112, maximum 24.73  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB144/AB144_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB144/AB144_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB145

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB145/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
13 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB145/AB145_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB145/AB145_contacts_hbonds_rot.mp4  
  
Changed 8741 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB145/AB145_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB145/AB145_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -18.14, mean
-2.33, maximum 14.80  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -26.69, mean
-0.93, maximum 18.07  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB145/AB145_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB145/AB145_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -28.01, mean
-5.401, maximum 21.62  
Map values for surface ""best_model.pdb_B SES surface"": minimum -30.61, mean
-4.308, maximum 24.44  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB145/AB145_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB145/AB145_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB146

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB146/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
18 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB146/AB146_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB146/AB146_contacts_hbonds_rot.mp4  
  
Changed 9350 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB146/AB146_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB146/AB146_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.03, mean
-2.31, maximum 9.58  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.94, mean
0.71, maximum 22.40  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB146/AB146_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB146/AB146_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -27.24, mean
-5.331, maximum 22.31  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.25, mean
-5.951, maximum 25.89  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB146/AB146_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB146/AB146_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB154

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB154/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
3 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB154/AB154_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB154/AB154_contacts_hbonds_rot.mp4  
  
Changed 22068 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB154/AB154_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB154/AB154_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -18.41, mean
-3.31, maximum 7.49  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -23.65, mean
-1.37, maximum 19.87  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB154/AB154_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB154/AB154_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -33.95, mean
-5.327, maximum 24.43  
Map values for surface ""best_model.pdb_B SES surface"": minimum -30.81, mean
-4.353, maximum 26.13  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB154/AB154_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AB154/AB154_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AC154

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AC154/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
6 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AC154/AC154_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AC154/AC154_contacts_hbonds_rot.mp4  
  
Changed 22066 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AC154/AC154_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AC154/AC154_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -22.13, mean
-2.64, maximum 8.46  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -22.65, mean
-1.36, maximum 23.87  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AC154/AC154_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AC154/AC154_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -27.13, mean
-6.166, maximum 21.88  
Map values for surface ""best_model.pdb_B SES surface"": minimum -32.92, mean
-4.26, maximum 25.79  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AC154/AC154_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AC154/AC154_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AD154

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AD154/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
2 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AD154/AD154_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AD154/AD154_contacts_hbonds_rot.mp4  
  
Changed 20772 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AD154/AD154_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AD154/AD154_sphere_rot.mp4  
  
Changed 0 atom styles  
Exception ignored in tp_clear of:   
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py"",
line 512, in cast  
return _cast(obj, obj, typ)  
^^^^^^^^^^^^^^^^^^^^  
TypeError: NoneType takes no arguments  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -12.70, mean
-0.54, maximum 9.74  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -21.26, mean
-1.37, maximum 23.05  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AD154/AD154_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AD154/AD154_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -29.81, mean
-3.865, maximum 22.51  
Map values for surface ""best_model.pdb_B SES surface"": minimum -36.18, mean
-4.329, maximum 24.39  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AD154/AD154_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AD154/AD154_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AE154

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AE154/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
0 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AE154/AE154_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AE154/AE154_contacts_hbonds_rot.mp4  
  
Changed 20547 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AE154/AE154_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AE154/AE154_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -6.90, mean
3.38, maximum 10.54  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -24.24, mean
-1.39, maximum 20.60  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AE154/AE154_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AE154/AE154_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -24.33, mean
-4.654, maximum 20.8  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.74, mean
-4.35, maximum 25.74  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AE154/AE154_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AE154/AE154_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF142

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF142/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
10 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF142/AF142_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF142/AF142_contacts_hbonds_rot.mp4  
  
Changed 13061 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF142/AF142_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF142/AF142_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.34, mean
-4.25, maximum 16.87  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -18.71, mean
1.14, maximum 20.13  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF142/AF142_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF142/AF142_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -27.89, mean
-4.741, maximum 27.78  
Map values for surface ""best_model.pdb_B SES surface"": minimum -30.14, mean
-3.724, maximum 25.43  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF142/AF142_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF142/AF142_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF143

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF143/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
18 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF143/AF143_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF143/AF143_contacts_hbonds_rot.mp4  
  
Changed 13132 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF143/AF143_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF143/AF143_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -34.18, mean
-4.58, maximum 22.93  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -22.22, mean
0.71, maximum 19.50  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF143/AF143_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF143/AF143_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -29.02, mean
-4.739, maximum 25.4  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.82, mean
-3.607, maximum 26.36  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF143/AF143_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF143/AF143_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF144

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF144/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
8 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF144/AF144_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF144/AF144_contacts_hbonds_rot.mp4  
  
Changed 13384 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF144/AF144_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF144/AF144_sphere_rot.mp4  
  
Changed 0 atom styles  
Exception ignored in tp_clear of:   
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molarray.py"", line 161, in __iter__  
self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: NoneType takes no arguments  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -27.91, mean
-5.01, maximum 14.98  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -22.18, mean
-3.32, maximum 13.20  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF144/AF144_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF144/AF144_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -33.08, mean
-5.066, maximum 31.21  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.39, mean
-5.156, maximum 25.42  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF144/AF144_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF144/AF144_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF145

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF145/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
9 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF145/AF145_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF145/AF145_contacts_hbonds_rot.mp4  
  
Changed 13273 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF145/AF145_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF145/AF145_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -33.46, mean
-3.98, maximum 18.91  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.95, mean
-0.86, maximum 14.05  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF145/AF145_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF145/AF145_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -29.06, mean
-5.113, maximum 28.08  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.78, mean
-4.243, maximum 26.06  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF145/AF145_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF145/AF145_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF146

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF146/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
24 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF146/AF146_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF146/AF146_contacts_hbonds_rot.mp4  
  
Changed 13882 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF146/AF146_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF146/AF146_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.27, mean
-5.66, maximum 17.42  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.30, mean
0.71, maximum 21.83  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF146/AF146_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF146/AF146_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -34.77, mean
-5.117, maximum 25.54  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.56, mean
-5.906, maximum 32.05  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF146/AF146_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF146/AF146_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF168

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF168/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
8 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF168/AF168_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF168/AF168_contacts_hbonds_rot.mp4  
  
Changed 13384 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF168/AF168_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF168/AF168_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -27.91, mean
-5.01, maximum 14.98  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -22.18, mean
-3.32, maximum 13.20  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF168/AF168_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF168/AF168_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -33.08, mean
-5.066, maximum 31.21  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.39, mean
-5.156, maximum 25.42  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF168/AF168_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF168/AF168_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AF181

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF181/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
5 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF181/AF181_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF181/AF181_contacts_hbonds_rot.mp4  
  
Changed 14678 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF181/AF181_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF181/AF181_sphere_rot.mp4  
  
Changed 0 atom styles  
Exception ignored in tp_clear of:   
Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molarray.py"", line 161, in   
self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers]  
^^^^^^^^^^^^^^^^^^^^^  
TypeError: NoneType takes no arguments  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.40, mean
-4.89, maximum 13.16  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -23.21, mean
-0.12, maximum 24.59  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF181/AF181_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF181/AF181_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -31.27, mean
-4.799, maximum 26.94  
Map values for surface ""best_model.pdb_B SES surface"": minimum -31.08, mean
-3.216, maximum 30.37  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AF181/AF181_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AF181/AF181_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AG145

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG145/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
6 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG145/AG145_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG145/AG145_contacts_hbonds_rot.mp4  
  
Changed 12726 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG145/AG145_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG145/AG145_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.32, mean
-0.67, maximum 15.18  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.54, mean
-0.83, maximum 15.62  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG145/AG145_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG145/AG145_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -30.15, mean
-6.362, maximum 25.73  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.89, mean
-4.272, maximum 25.71  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG145/AG145_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG145/AG145_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AG146

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG146/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
11 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG146/AG146_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG146/AG146_contacts_hbonds_rot.mp4  
  
Changed 13335 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG146/AG146_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG146/AG146_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.66, mean
-0.88, maximum 18.69  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -19.89, mean
0.62, maximum 21.26  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG146/AG146_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG146/AG146_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -36.24, mean
-6.384, maximum 34.54  
Map values for surface ""best_model.pdb_B SES surface"": minimum -28.04, mean
-5.96, maximum 26.72  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG146/AG146_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG146/AG146_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AG181

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG181/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
4 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG181/AG181_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG181/AG181_contacts_hbonds_rot.mp4  
  
Changed 14131 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG181/AG181_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG181/AG181_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.80, mean
-0.98, maximum 14.16  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -21.84, mean
-0.05, maximum 17.03  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG181/AG181_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG181/AG181_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -29.62, mean
-6.328, maximum 22.84  
Map values for surface ""best_model.pdb_B SES surface"": minimum -29.94, mean
-3.176, maximum 26.15  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AG181/AG181_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../AG181/AG181_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T110

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T110/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
2 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T110/T110_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T110/T110_contacts_hbonds_rot.mp4  
  
Changed 976 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T110/T110_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T110/T110_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -24.38, mean
-5.03, maximum 11.80  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.05, mean
-1.92, maximum 8.70  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T110/T110_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T110/T110_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -24.79, mean
-4.585, maximum 26.65  
Map values for surface ""best_model.pdb_B SES surface"": minimum -24.53, mean
-3.829, maximum 21.55  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T110/T110_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T110/T110_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T111

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T111/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
5 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T111/T111_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T111/T111_contacts_hbonds_rot.mp4  
  
Changed 1078 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T111/T111_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T111/T111_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -29.24, mean
-5.12, maximum 11.67  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -9.67, mean
1.37, maximum 10.28  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T111/T111_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T111/T111_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -32.58, mean
-4.732, maximum 23.59  
Map values for surface ""best_model.pdb_B SES surface"": minimum -23.66, mean
-2.954, maximum 22.08  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T111/T111_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T111/T111_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T112

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T112/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
2 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T112/T112_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T112/T112_contacts_hbonds_rot.mp4  
  
Changed 1236 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T112/T112_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T112/T112_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -42.99, mean
-4.78, maximum 11.84  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -8.35, mean
1.64, maximum 11.07  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T112/T112_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T112/T112_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -28.68, mean
-5.553, maximum 22.63  
Map values for surface ""best_model.pdb_B SES surface"": minimum -27.15, mean
-1.845, maximum 24.91  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T112/T112_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T112/T112_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T113

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T113/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
6 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T113/T113_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T113/T113_contacts_hbonds_rot.mp4  
  
Changed 1287 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T113/T113_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T113/T113_sphere_rot.mp4  
  
Changed 0 atom styles  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -24.67, mean
-5.38, maximum 11.68  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -7.56, mean
5.09, maximum 19.40  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right ""color key""

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T113/T113_coulombic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T113/T113_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface ""best_model.pdb_A SES surface"": minimum -31.32, mean
-5.629, maximum 23.55  
Map values for surface ""best_model.pdb_B SES surface"": minimum -23.39, mean
-2.007, maximum 21.7  

> key lipophilicity :-20 :0 :20 showTool true

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T113/T113_hydrophobic.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T113/T113_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T114

> ui mousemode right translate

> open ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/best_model.pdb""

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
2 hydrogen bonds found  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_contacts_hbonds.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T114/T114_contacts_hbonds_rot.mp4  
  
Changed 1591 atom styles  

> save ""/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_sphere.jpg""
> supersample 2

Movie saved to /Users/neyrinck/.../T114/T114_sphere_rot.mp4  
  
Changed 0 atom styles  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 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: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14W00106LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 9 days, 13 hours, 14 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      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


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.10.5
    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: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    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: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    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
    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: 1.1.8
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    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: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

}}}
"	defect	closed	normal		Core		duplicate						all	ChimeraX