Graphics crash, macOS 13.1, Intel Iris Plus Graphics

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x0000700012785000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700011782000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001077f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070000f77c000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070000e779000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070000d776000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070000c773000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007ff84b3b28c0 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2744 in update_buffer_data
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1912 in update_buffers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1924 in activate_bindings
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 814 in _draw_geometry
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259 in _draw_scene
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.morph._morph, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 61)


{"app_name":"ChimeraX","timestamp":"2024-12-02 14:17:13.00 -0500","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","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 13.1 (22C65)","roots_installed":0,"name":"ChimeraX","incident_id":"3DF0C88E-7D4E-4FF9-A77D-7062077B1D1C"}
{
  "uptime" : 1100000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir9,1",
  "coalitionID" : 18915,
  "osVersion" : {
    "train" : "macOS 13.1",
    "build" : "22C65",
    "releaseType" : "User"
  },
  "captureTime" : "2024-12-02 14:17:01.6223 -0500",
  "incident" : "3DF0C88E-7D4E-4FF9-A77D-7062077B1D1C",
  "pid" : 15074,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-12-02 13:16:05.8733 -0500",
  "procStartAbsTime" : 1125205110810243,
  "procExitAbsTime" : 1128860553734946,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"37268965-EBF2-5F29-A4CB-3567ADB20645","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "B920B223-42B7-E15E-B229-E6A9CE21DED5",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 3981,
  "bridgeVersion" : {"build":"21P1069","train":"8.1"},
  "sleepWakeUUID" : "4A0B4613-50AC-4719-B559-C7F3A9D7CF8E",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
  "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,
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    "uuid" : "f314b62b-98f4-3a7c-8296-8739f8b6855a",
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    "name" : "libsystem_platform.dylib"
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    "source" : "A",
    "base" : 0,
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    "name" : "libGPUSupportMercury.dylib"
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    "arch" : "x86_64",
    "base" : 140712108212224,
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    "size" : 16089088,
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    "path" : "\/System\/Library\/Extensions\/AppleIntelICLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelICLGraphicsGLDriver",
    "name" : "AppleIntelICLGraphicsGLDriver",
    "CFBundleVersion" : "20.0.2"
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    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
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    "uuid" : "ed442788-783e-39d6-b7c5-b385191e8366",
    "path" : "\/usr\/lib\/libffi.dylib",
    "name" : "libffi.dylib"
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so",
    "name" : "_queue.cpython-311-darwin.so"
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    "source" : "P",
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    "size" : 32768,
    "uuid" : "ce09d1ac-f6df-3770-9dda-8f52871a152d",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/select.cpython-311-darwin.so",
    "name" : "select.cpython-311-darwin.so"
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4825088,
    "uuid" : "beb5fc0b-7196-3c1d-a59a-f62ada98f592",
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    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.300"
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    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 16809984,
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    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
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    "uuid" : "5c425ea0-066d-38b9-9db4-8d3885d78b6b",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  },
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    "uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
  }
],
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=12.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=12.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 2160K        4 \nCG image                           448K       55 \nColorSync                          252K       29 \nCoreAnimation                      268K       21 \nCoreGraphics                        12K        2 \nCoreServices                       624K        2 \nCoreUI image data                 5168K       40 \nFoundation                          32K        2 \nIOKit                             7940K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                            11.5G     3718 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        128K       32 \nStack                            260.2M       33 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      241.6M      270 \n__CTF                               756        1 \n__DATA                            41.6M      778 \n__DATA_CONST                      50.0M      444 \n__DATA_DIRTY                      1881K      239 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       212.9M      159 \n__OBJC_RO                         65.4M        1 \n__OBJC_RW                         1988K        2 \n__TEXT                           945.9M      787 \ndyld private memory                288K        2 \nmapped file                      527.1M       71 \nshared memory                     3000K       30 \n===========                     =======  ======= \nTOTAL                             14.3G     6747 \nTOTAL, minus reserved VM space    13.9G     6747 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "62b4513af75dc926494899c6",
      "factorPackIds" : {
        "COREOS_ICD" : "62fbe3cfa9a700130f60b3ea"
      },
      "deploymentId" : 240000019
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000448
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
      "experimentId" : "6643969b3099cf28e049862f",
      "deploymentId" : 400000007
    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== 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 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2plv fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 2plv fetched from pdbe_bio  
---  
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
1 messages similar to the above omitted  
notes | Fetching compressed 2plv bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/2plv-assembly-1.cif.gz  
Fetching CCD SPH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/SPH/SPH.cif  
Fetching CCD MYR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/MYR/MYR.cif  
Fetching compressed 2plv bioassembly 2 from
https://www.ebi.ac.uk/pdbe/static/entry/download/2plv-assembly-2.cif.gz  
Fetching compressed 2plv bioassembly 3 from
https://www.ebi.ac.uk/pdbe/static/entry/download/2plv-assembly-3.cif.gz  
Fetching compressed 2plv bioassembly 4 from
https://www.ebi.ac.uk/pdbe/static/entry/download/2plv-assembly-4.cif.gz  
Fetching compressed 2plv bioassembly 5 from
https://www.ebi.ac.uk/pdbe/static/entry/download/2plv-assembly-5.cif.gz  
Fetching compressed 2plv bioassembly 6 from
https://www.ebi.ac.uk/pdbe/static/entry/download/2plv-assembly-6.cif.gz  
  
2plv bioassembly 1 title:  
Structural factors that control conformational transitions and serotype
specificity In type 3 poliovirus [more info...]  
  
Chain information for 2plv bioassembly 1 #1.1  
---  
Chain | Description  
A AA AAA AAB AAC AAD AAE AAF AAG AAH AAI AAJ AAK AAL AAM AAN AAO AAP AAQ AAR AAS AAT AAU AAV AAW AAX AAY AAZ AB ABA ABB ABC ABD ABE ABF ABG AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)  
B BA BAA BAB BAC BAD BAE BAF BAG BAH BAI BAJ BAK BAL BAM BAN BAO BAP BAQ BAR BAS BAT BAU BAV BAW BAX BAY BAZ BB BBA BBB BBC BBD BBE BBF BBG BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)  
C CA CAA CAB CAC CAD CAE CAF CAG CAH CAI CAJ CAK CAL CAM CAN CAO CAP CAQ CAR CAS CAT CAU CAV CAW CAX CAY CAZ CB CBA CBB CBC CBD CBE CBF CBG CC CD CE CF CG CH CI CJ CK CL CM CN CO CP CQ CR CS CT CU CV CW CX CY CZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)  
D DA DAA DAB DAC DAD DAE DAF DAG DAH DAI DAJ DAK DAL DAM DAN DAO DAP DAQ DAR DAS DAT DAU DAV DAW DAX DAY DAZ DB DBA DBB DBC DBD DBE DBF DBG DC DD DE DF DG DH DI DJ DK DL DM DN DO DP DQ DR DS DT DU DV DW DX DY DZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)  
  
Non-standard residues in 2plv bioassembly 1 #1.1  
---  
MYR — (MYR)  
SPH — (SPH)  
  
2plv bioassembly 1 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
2plv bioassembly 2 title:  
Structural factors that control conformational transitions and serotype
specificity In type 3 poliovirus [more info...]  
  
Chain information for 2plv bioassembly 2 #1.2  
---  
Chain | Description  
A | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)  
B | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)  
C | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)  
D | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)  
  
Non-standard residues in 2plv bioassembly 2 #1.2  
---  
MYR — (MYR)  
SPH — (SPH)  
  
2plv bioassembly 2 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
2plv bioassembly 3 title:  
Structural factors that control conformational transitions and serotype
specificity In type 3 poliovirus [more info...]  
  
Chain information for 2plv bioassembly 3 #1.3  
---  
Chain | Description  
A AA AB AC AD | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)  
B BA BB BC BD | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)  
C CA CB CC CD | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)  
D DA DB DC DD | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)  
  
Non-standard residues in 2plv bioassembly 3 #1.3  
---  
MYR — (MYR)  
SPH — (SPH)  
  
2plv bioassembly 3 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
2plv bioassembly 4 title:  
Structural factors that control conformational transitions and serotype
specificity In type 3 poliovirus [more info...]  
  
Chain information for 2plv bioassembly 4 #1.4  
---  
Chain | Description  
A AA AB AC AD AE | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)  
B BA BB BC BD BE | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)  
C CA CB CC CD CE | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)  
D DA DB DC DD DE | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)  
  
Non-standard residues in 2plv bioassembly 4 #1.4  
---  
MYR — (MYR)  
SPH — (SPH)  
  
2plv bioassembly 4 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
2plv bioassembly 5 title:  
Structural factors that control conformational transitions and serotype
specificity In type 3 poliovirus [more info...]  
  
Chain information for 2plv bioassembly 5 #1.5  
---  
Chain | Description  
A | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)  
B | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)  
C | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)  
D | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)  
  
Non-standard residues in 2plv bioassembly 5 #1.5  
---  
MYR — (MYR)  
SPH — (SPH)  
  
2plv bioassembly 5 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
2plv bioassembly 6 title:  
Structural factors that control conformational transitions and serotype
specificity In type 3 poliovirus [more info...]  
  
Chain information for 2plv bioassembly 6 #1.6  
---  
Chain | Description  
A AA AAA AAB AAC AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP1)  
B BA BAA BAB BAC BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP2)  
C CA CAA CAB CAC CB CC CD CE CF CG CH CI CJ CK CL CM CN CO CP CQ CR CS CT CU CV CW CX CY CZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP3)  
D DA DAA DAB DAC DB DC DD DE DF DG DH DI DJ DK DL DM DN DO DP DQ DR DS DT DU DV DW DX DY DZ | HUMAN POLIOVIRUS TYPE 1 (SUBUNIT VP4)  
  
Non-standard residues in 2plv bioassembly 6 #1.6  
---  
MYR — (MYR)  
SPH — (SPH)  
  
2plv bioassembly 6 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
Opened 6 biological assemblies for 2plv  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> hide #!1.4 models

> hide #!1.5 models

> hide #!1.6 models

> close #1.2

> close #1.3

> close #1.4-6

> color white

> select /A

2251 atoms, 2313 bonds, 1 pseudobond, 288 residues, 2 models selected  

> color (#!1.1 & sel) red

> select /B

2085 atoms, 2142 bonds, 268 residues, 1 model selected  

> color sel blue

> select /C

1834 atoms, 1881 bonds, 235 residues, 1 model selected  

> color sel yellow

> select /D

477 atoms, 484 bonds, 1 pseudobond, 63 residues, 2 models selected  

> color (#!1.1 & sel) hot pink

> close session

> open 1ppi fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 1ppi fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 1ppi bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/1ppi-assembly-1.cif.gz  
Fetching CCD GLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/GLC/GLC.cif  
Fetching CCD BGC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/BGC/BGC.cif  
Fetching CCD DAF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/DAF/DAF.cif  
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
  
1ppi bioassembly 1 title:  
The active center of A mammalian α-amylase. The structure of the complex of A
pancreatic α-amylase with A carbohydrate inhibitor refined to 2.2 angstroms
resolution [more info...]  
  
Chain information for 1ppi bioassembly 1 #1  
---  
Chain | Description  
A | ALPHA-AMYLASE  
  
Non-standard residues in 1ppi bioassembly 1 #1  
---  
BGC — (BGC)  
CA — (CA)  
CL — (CL)  
DAF — (DAF)  
GLC — (GLC)  
  
Opened 1 biological assemblies for 1ppi  

> ui tool show Distances

Drag select of 11 residues  

> hide sel cartoons

> show sel atoms

Exactly two atoms must be selected!  

> select clear

> select /A:223@O

1 atom, 1 residue, 1 model selected  

> select add /A:88@O

2 atoms, 2 residues, 1 model selected  

> distance /A:223@O /A:88@O

Distance between /A PRO 223 O and ASN 88 O: 16.248Å  

> close #2

> close session

> open 7x5v fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 7x5v fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 7x5v bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/7x5v-assembly-1.cif.gz  
  
7x5v bioassembly 1 title:  
NaVEh Sodium channel, and NaVEh from the coccolithophore Emiliania huxleyi
[more info...]  
  
Chain information for 7x5v bioassembly 1 #1  
---  
Chain | Description  
A B C D | ion channel,GFP-TwinStrep  
E | ion channel  
  
Opened 1 biological assemblies for 7x5v  
Drag select of 9504 atoms  

> show sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel surfaces

> select clear

> ui tool show "Side View"

> close session

> open 6idp fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6idp fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching compressed 6idp bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6idp-assembly-1.cif.gz  
Fetching CCD OLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OLC/OLC.cif  
  
6idp bioassembly 1 title:  
Crystal structure of Vibrio cholerae MATE transporter VcmN in the straight
form [more info...]  
  
Chain information for 6idp bioassembly 1 #1  
---  
Chain | Description  
A | MATE family efflux transporter  
  
Non-standard residues in 6idp bioassembly 1 #1  
---  
OLC — (OLC)  
  
Opened 1 biological assemblies for 6idp  

> open 6idr fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6idr fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6idr bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6idr-assembly-1.cif.gz  
  
6idr bioassembly 1 title:  
Crystal structure of Vibrio cholerae MATE transporter VcmN in the bent form
[more info...]  
  
Chain information for 6idr bioassembly 1 #2  
---  
Chain | Description  
A | MATE family efflux transporter  
  
Non-standard residues in 6idr bioassembly 1 #2  
---  
OLC — (OLC)  
  
Opened 1 biological assemblies for 6idr  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6idp bioassembly 1, chain A (#1) with 6idr bioassembly 1, chain A
(#2), sequence alignment score = 2262.6  
RMSD between 409 pruned atom pairs is 0.760 angstroms; (across all 438 pairs:
1.244)  
  

>

Unknown command: modeller #1,2 frames 40  

> morph #1,2 frames 40

Computed 41 frame morph #3  

> coordset #3 1,41

> movie record

> movie stop

> movie encode /Users/claudiabocz/Desktop/movie.mp4

Movie saved to /Users/claudiabocz/Desktop/movie.mp4  
  

> close session

> open 4OQ8 fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 4OQ8 fetched from pdbe_bio  
---  
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
1 messages similar to the above omitted  
notes | Fetching compressed 4OQ8 bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/4oq8-assembly-1.cif.gz  
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Combining 3 symmetry atoms into HOH /IR:301 O  
Combining 3 symmetry atoms into HOH /IAD:301 O  
Combining 3 symmetry atoms into HOH /IJ:301 O  
Combining 3 symmetry atoms into HOH /IQ:301 O  
Combining 3 symmetry atoms into HOH /IAH:301 O  
15 messages similar to the above omitted  
Fetching compressed 4OQ8 bioassembly 2 from
https://www.ebi.ac.uk/pdbe/static/entry/download/4oq8-assembly-2.cif.gz  
Fetching compressed 4OQ8 bioassembly 3 from
https://www.ebi.ac.uk/pdbe/static/entry/download/4oq8-assembly-3.cif.gz  
Fetching compressed 4OQ8 bioassembly 4 from
https://www.ebi.ac.uk/pdbe/static/entry/download/4oq8-assembly-4.cif.gz  
Combining 3 symmetry atoms into HOH /I:301 O  
Fetching compressed 4OQ8 bioassembly 5 from
https://www.ebi.ac.uk/pdbe/static/entry/download/4oq8-assembly-5.cif.gz  
Fetching compressed 4OQ8 bioassembly 6 from
https://www.ebi.ac.uk/pdbe/static/entry/download/4oq8-assembly-6.cif.gz  
Combining 2 symmetry atoms into HOH /ID:301 O  
Combining 2 symmetry atoms into HOH /IH:301 O  
Combining 3 symmetry atoms into HOH /I:301 O  
Combining 2 symmetry atoms into HOH /IA:301 O  
  
4OQ8 bioassembly 1 title:  
Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral
constraints [more info...]  
  
Chain information for 4OQ8 bioassembly 1 #1.1  
---  
Chain | Description  
A AA AAA AAB AAC AAD AAE AAF AAG AAH AAI AAJ AAK AAL AAM AAN AAO AAP AAQ AAR AAS AAT AAU AAV AAW AAX AAY AAZ AB ABA ABB ABC ABD ABE ABF ABG AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ | Coat protein  
B BA BAA BAB BAC BAD BAE BAF BAG BAH BAI BAJ BAK BAL BAM BAN BAO BAP BAQ BAR BAS BAT BAU BAV BAW BAX BAY BAZ BB BBA BBB BBC BBD BBE BBF BBG BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')  
C CA CAA CAB CAC CAD CAE CAF CAG CAH CAI CAJ CAK CAL CAM CAN CAO CAP CAQ CAR CAS CAT CAU CAV CAW CAX CAY CAZ CB CBA CBB CBC CBD CBE CBF CBG CC CD CE CF CG CH CI CJ CK CL CM CN CO CP CQ CR CS CT CU CV CW CX CY CZ | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')  
D DA DAA DAB DAC DAD DAE DAF DAG DAH DAI DAJ DAK DAL DAM DAN DAO DAP DAQ DAR DAS DAT DAU DAV DAW DAX DAY DAZ DB DBA DBB DBC DBD DBE DBF DBG DC DD DE DF DG DH DI DJ DK DL DM DN DO DP DQ DR DS DT DU DV DW DX DY DZ | RNA (5'-R(P*UP*U)-3')  
  
Non-standard residues in 4OQ8 bioassembly 1 #1.1  
---  
MG — (MG)  
PO4 — (PO4)  
SO4 — (SO4)  
  
4OQ8 bioassembly 1 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
34680 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
4OQ8 bioassembly 2 title:  
Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral
constraints [more info...]  
  
Chain information for 4OQ8 bioassembly 2 #1.2  
---  
Chain | Description  
A | Coat protein  
B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')  
C | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')  
D | RNA (5'-R(P*UP*U)-3')  
  
Non-standard residues in 4OQ8 bioassembly 2 #1.2  
---  
MG — (MG)  
PO4 — (PO4)  
SO4 — (SO4)  
  
4OQ8 bioassembly 2 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
578 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
4OQ8 bioassembly 3 title:  
Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral
constraints [more info...]  
  
Chain information for 4OQ8 bioassembly 3 #1.3  
---  
Chain | Description  
A AA AB AC AD | Coat protein  
B BA BB BC BD | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')  
C CA CB CC CD | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')  
D DA DB DC DD | RNA (5'-R(P*UP*U)-3')  
  
Non-standard residues in 4OQ8 bioassembly 3 #1.3  
---  
MG — (MG)  
PO4 — (PO4)  
SO4 — (SO4)  
  
4OQ8 bioassembly 3 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
2890 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
4OQ8 bioassembly 4 title:  
Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral
constraints [more info...]  
  
Chain information for 4OQ8 bioassembly 4 #1.4  
---  
Chain | Description  
A AA AB AC AD AE | Coat protein  
B BA BB BC BD BE | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')  
C CA CB CC CD CE | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')  
D DA DB DC DD DE | RNA (5'-R(P*UP*U)-3')  
  
Non-standard residues in 4OQ8 bioassembly 4 #1.4  
---  
MG — (MG)  
PO4 — (PO4)  
SO4 — (SO4)  
  
4OQ8 bioassembly 4 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
3468 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
4OQ8 bioassembly 5 title:  
Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral
constraints [more info...]  
  
Chain information for 4OQ8 bioassembly 5 #1.5  
---  
Chain | Description  
A | Coat protein  
B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')  
C | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')  
D | RNA (5'-R(P*UP*U)-3')  
  
Non-standard residues in 4OQ8 bioassembly 5 #1.5  
---  
MG — (MG)  
PO4 — (PO4)  
SO4 — (SO4)  
  
4OQ8 bioassembly 5 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
578 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
4OQ8 bioassembly 6 title:  
Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral
constraints [more info...]  
  
Chain information for 4OQ8 bioassembly 6 #1.6  
---  
Chain | Description  
A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN | Coat protein  
B BA BB BC BD BE BF BG BH BI BJ BK BL BM BN | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')  
C CA CB CC CD CE CF CG CH CI CJ CK CL CM CN | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')  
D DA DB DC DD DE DF DG DH DI DJ DK DL DM DN | RNA (5'-R(P*UP*U)-3')  
  
Non-standard residues in 4OQ8 bioassembly 6 #1.6  
---  
MG — (MG)  
PO4 — (PO4)  
SO4 — (SO4)  
  
4OQ8 bioassembly 6 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
8670 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Opened 6 biological assemblies for 4OQ8  

> close #1.2-6

> select ::name="HOH"::name="MG"::name="PO4"::name="SO4"

17540 atoms, 720 bonds, 16820 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select
> /A/AA/AAA/AAB/AAC/AAD/AAE/AAF/AAG/AAH/AAI/AAJ/AAK/AAL/AAM/AAN/AAO/AAP/AAQ/AAR/AAS/AAT/AAU/AAV/AAW/AAX/AAY/AAZ/AB/ABA/ABB/ABC/ABD/ABE/ABF/ABG/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ

67080 atoms, 68520 bonds, 8640 residues, 1 model selected  

> color sel red

> select clear

> select
> /B/BA/BAA/BAB/BAC/BAD/BAE/BAF/BAG/BAH/BAI/BAJ/BAK/BAL/BAM/BAN/BAO/BAP/BAQ/BAR/BAS/BAT/BAU/BAV/BAW/BAX/BAY/BAZ/BB/BBA/BBB/BBC/BBD/BBE/BBF/BBG/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/BO/BP/BQ/BR/BS/BT/BU/BV/BW/BX/BY/BZ

13260 atoms, 15000 bonds, 600 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select
> /D/DA/DAA/DAB/DAC/DAD/DAE/DAF/DAG/DAH/DAI/DAJ/DAK/DAL/DAM/DAN/DAO/DAP/DAQ/DAR/DAS/DAT/DAU/DAV/DAW/DAX/DAY/DAZ/DB/DBA/DBB/DBC/DBD/DBE/DBF/DBG/DC/DD/DE/DF/DG/DH/DI/DJ/DK/DL/DM/DN/DO/DP/DQ/DR/DS/DT/DU/DV/DW/DX/DY/DZ

1560 atoms, 1620 bonds, 120 residues, 1 model selected  

> color sel cornflower blue

> select
> /C/CA/CAA/CAB/CAC/CAD/CAE/CAF/CAG/CAH/CAI/CAJ/CAK/CAL/CAM/CAN/CAO/CAP/CAQ/CAR/CAS/CAT/CAU/CAV/CAW/CAX/CAY/CAZ/CB/CBA/CBB/CBC/CBD/CBE/CBF/CBG/CC/CD/CE/CF/CG/CH/CI/CJ/CK/CL/CM/CN/CO/CP/CQ/CR/CS/CT/CU/CV/CW/CX/CY/CZ

12060 atoms, 13200 bonds, 600 residues, 1 model selected  

> color sel cornflower blue

> select
> /A/AA/AAA/AAB/AAC/AAD/AAE/AAF/AAG/AAH/AAI/AAJ/AAK/AAL/AAM/AAN/AAO/AAP/AAQ/AAR/AAS/AAT/AAU/AAV/AAW/AAX/AAY/AAZ/AB/ABA/ABB/ABC/ABD/ABE/ABF/ABG/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ

67080 atoms, 68520 bonds, 8640 residues, 1 model selected  

> color sel orange

> color sel hot pink

> select clear

Drag select of 93960 atoms, 1620 bonds  

> show sel surfaces

> hide sel cartoons

> select clear

> ui tool show "Side View"

> save "/Users/claudiabocz/Desktop/class 10 Q2.png" width 864 height 594
> supersample 3 transparentBackground true

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting simple

Drag select of 4OQ8 bioassembly 1_ABA SES surface, 32 of 146784 triangles,
4OQ8 bioassembly 1_AH SES surface, 3890 of 146908 triangles, 4OQ8 bioassembly
1_AX SES surface, 1892 of 146176 triangles, 4OQ8 bioassembly 1_BH SES surface,
1034 of 34968 triangles, 4OQ8 bioassembly 1_CBB SES surface, 1022 of 33854
triangles, 60 atoms  
Drag select of 4OQ8 bioassembly 1_ABA SES surface, 986 of 146784 triangles,
4OQ8 bioassembly 1_ABB SES surface, 1652 of 147020 triangles, 4OQ8 bioassembly
1_AH SES surface, 17207 of 146908 triangles, 4OQ8 bioassembly 1_AX SES
surface, 4930 of 146176 triangles, 4OQ8 bioassembly 1_BBB SES surface, 757 of
34940 triangles, 4OQ8 bioassembly 1_BH SES surface, 5859 of 34968 triangles,
4OQ8 bioassembly 1_CBB SES surface, 6112 of 33854 triangles, 4OQ8 bioassembly
1_CH SES surface, 548 of 33878 triangles, 303 atoms  

> style sel ball

Changed 303 atom styles  

> hide sel surfaces

> select clear

Drag select of 4OQ8 bioassembly 1_AAH SES surface, 10307 of 147192 triangles,
4OQ8 bioassembly 1_AAV SES surface, 11449 of 146758 triangles, 4OQ8
bioassembly 1_AAW SES surface, 90 of 147112 triangles, 4OQ8 bioassembly 1_AC
SES surface, 12597 of 148128 triangles, 4OQ8 bioassembly 1_BAH SES surface,
208 of 34942 triangles, 4OQ8 bioassembly 1_BC SES surface, 545 of 34970
triangles, 4OQ8 bioassembly 1_CAV SES surface, 294 of 33798 triangles, 4OQ8
bioassembly 1_CAW SES surface, 523 of 33818 triangles, 4OQ8 bioassembly 1_DAV
SES surface, 328 of 5514 triangles, 234 atoms  

> style sel ball

Changed 234 atom styles  

> hide sel surfaces

> select clear

> ui tool show Distances

> select clear

> select add /AAV:109@CD1

1 atom, 1 residue, 1 model selected  

> select add /AH:158@CD2

2 atoms, 2 residues, 1 model selected  

> distance /AAV:109@CD1 /AH:158@CD2

Distance between /AAV PHE 109 CD1 and /AH PHE 158 CD2: 121.221Å  

> select
> /B/BA/BAA/BAB/BAC/BAD/BAE/BAF/BAG/BAH/BAI/BAJ/BAK/BAL/BAM/BAN/BAO/BAP/BAQ/BAR/BAS/BAT/BAU/BAV/BAW/BAX/BAY/BAZ/BB/BBA/BBB/BBC/BBD/BBE/BBF/BBG/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/BO/BP/BQ/BR/BS/BT/BU/BV/BW/BX/BY/BZ

13260 atoms, 15000 bonds, 600 residues, 1 model selected  

> hide (#!1.1 & sel) target a

> select
> /D/DA/DAA/DAB/DAC/DAD/DAE/DAF/DAG/DAH/DAI/DAJ/DAK/DAL/DAM/DAN/DAO/DAP/DAQ/DAR/DAS/DAT/DAU/DAV/DAW/DAX/DAY/DAZ/DB/DBA/DBB/DBC/DBD/DBE/DBF/DBG/DC/DD/DE/DF/DG/DH/DI/DJ/DK/DL/DM/DN/DO/DP/DQ/DR/DS/DT/DU/DV/DW/DX/DY/DZ

1560 atoms, 1620 bonds, 120 residues, 1 model selected  

> hide (#!1.1 & sel) target a

> select
> /C/CA/CAA/CAB/CAC/CAD/CAE/CAF/CAG/CAH/CAI/CAJ/CAK/CAL/CAM/CAN/CAO/CAP/CAQ/CAR/CAS/CAT/CAU/CAV/CAW/CAX/CAY/CAZ/CB/CBA/CBB/CBC/CBD/CBE/CBF/CBG/CC/CD/CE/CF/CG/CH/CI/CJ/CK/CL/CM/CN/CO/CP/CQ/CR/CS/CT/CU/CV/CW/CX/CY/CZ

12060 atoms, 13200 bonds, 600 residues, 1 model selected  

> hide (#!1.1 & sel) target a

> select clear

> hide surfaces

Drag select of 34520 atoms, 524 bonds, 1 pseudobonds  

> style sel ball

Changed 34520 atom styles  

> select clear

> close #2

Drag select of 34234 atoms, 25954 bonds  

> style sel ball

Changed 34234 atom styles  

> select clear

> select
> /A/AA/AAA/AAB/AAC/AAD/AAE/AAF/AAG/AAH/AAI/AAJ/AAK/AAL/AAM/AAN/AAO/AAP/AAQ/AAR/AAS/AAT/AAU/AAV/AAW/AAX/AAY/AAZ/AB/ABA/ABB/ABC/ABD/ABE/ABF/ABG/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ

67080 atoms, 68520 bonds, 8640 residues, 1 model selected  

> style sel ball

Changed 67080 atom styles  

> select clear

> select /AAY:86@CB

1 atom, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> select /AAY:85@OG1

1 atom, 1 residue, 1 model selected  

> select add /AAU:148@NH1

2 atoms, 2 residues, 2 models selected  

> distance /AAY:85@OG1 /AAU:148@NH1

Distance between /AAY THR 85 OG1 and /AAU ARG 148 NH1 (alt loc A): 167.877Å  

> distance style radius 3

> distance style radius 2

> distance style radius 0.5

> close #2

> select clear

> select /AAJ:22@CG

1 atom, 1 residue, 1 model selected  

> select add /ABB:144@N

2 atoms, 2 residues, 2 models selected  

> distance /AAJ:22@CG /ABB:144@N

Distance between /AAJ MET 22 CG (alt loc A) and /ABB ARG 144 N: 134.555Å  

> close #2

Drag select of 34280 atoms, 35016 bonds  

> show sel surfaces

> select
> /A/AA/AAA/AAB/AAC/AAD/AAE/AAF/AAG/AAH/AAI/AAJ/AAK/AAL/AAM/AAN/AAO/AAP/AAQ/AAR/AAS/AAT/AAU/AAV/AAW/AAX/AAY/AAZ/AB/ABA/ABB/ABC/ABD/ABE/ABF/ABG/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ

67080 atoms, 68520 bonds, 8640 residues, 1 model selected  

> show sel surfaces

> select clear

Drag select of 4OQ8 bioassembly 1_AAF SES surface, 879 of 146764 triangles,
4OQ8 bioassembly 1_AAG SES surface, 11268 of 147162 triangles, 4OQ8
bioassembly 1_AAH SES surface, 71 of 147192 triangles, 4OQ8 bioassembly 1_AAV
SES surface, 7329 of 146758 triangles, cap near, 84 of 4106 triangles, 4OQ8
bioassembly 1_AD SES surface, 5575 of 146794 triangles, 256 atoms, 251 bonds  

> select clear

Drag select of 4OQ8 bioassembly 1_AAF SES surface, 9784 of 146764 triangles,
4OQ8 bioassembly 1_AAG SES surface, 19471 of 147162 triangles, 4OQ8
bioassembly 1_AAH SES surface, 2435 of 147192 triangles, 4OQ8 bioassembly
1_AAJ SES surface, 93 of 146262 triangles, cap near, 75 of 951 triangles, 4OQ8
bioassembly 1_AAV SES surface, 9249 of 146758 triangles, 4OQ8 bioassembly 1_AD
SES surface, 11671 of 146794 triangles, 391 atoms, 402 bonds  

> hide sel surfaces

> select clear

Drag select of 4OQ8 bioassembly 1_AAY SES surface, 2367 of 147414 triangles,
cap near, 54 of 5023 triangles, 4OQ8 bioassembly 1_AAZ SES surface, 12950 of
146040 triangles, cap near, 29 of 2291 triangles, 4OQ8 bioassembly 1_ABA SES
surface, 20638 of 146784 triangles, 4OQ8 bioassembly 1_AQ SES surface, 3663 of
146228 triangles, cap near, 191 of 4387 triangles, 4OQ8 bioassembly 1_AX SES
surface, 5543 of 146176 triangles, 4OQ8 bioassembly 1_AZ SES surface, 8473 of
147772 triangles, 401 atoms, 409 bonds  

> select clear

Drag select of 4OQ8 bioassembly 1_AAY SES surface, 92 of 147414 triangles,
4OQ8 bioassembly 1_AAZ SES surface, 8910 of 146040 triangles, cap near, 31 of
2291 triangles, 4OQ8 bioassembly 1_ABA SES surface, 21018 of 146784 triangles,
4OQ8 bioassembly 1_ABB SES surface, 270 of 147020 triangles, 4OQ8 bioassembly
1_AH SES surface, 747 of 146908 triangles, 4OQ8 bioassembly 1_AQ SES surface,
3220 of 146228 triangles, cap near, 161 of 4387 triangles, 4OQ8 bioassembly
1_AX SES surface, 7493 of 146176 triangles, 4OQ8 bioassembly 1_AZ SES surface,
7000 of 147772 triangles, 338 atoms, 337 bonds  

> select clear

Drag select of 4OQ8 bioassembly 1_AAZ SES surface, 4294 of 146040 triangles,
4OQ8 bioassembly 1_ABA SES surface, 23450 of 146784 triangles, 4OQ8
bioassembly 1_ABB SES surface, 5030 of 147020 triangles, 4OQ8 bioassembly 1_AH
SES surface, 8086 of 146908 triangles, 4OQ8 bioassembly 1_AQ SES surface, 3339
of 146228 triangles, cap near, 138 of 4387 triangles, 4OQ8 bioassembly 1_AX
SES surface, 9007 of 146176 triangles, 4OQ8 bioassembly 1_AZ SES surface, 4519
of 147772 triangles, 399 atoms, 409 bonds  

> select clear

Drag select of 4OQ8 bioassembly 1_AAZ SES surface, 29339 of 146040 triangles,
cap near, 1769 of 2628 triangles, 4OQ8 bioassembly 1_ABA SES surface, 6988 of
146784 triangles, 4OQ8 bioassembly 1_AX SES surface, 230 of 146176 triangles,
4OQ8 bioassembly 1_AZ SES surface, 330 of 147772 triangles, cap near, 95 of
480 triangles, 417 atoms, 422 bonds  

> style sel ball

Changed 417 atom styles  

> style sel ball

Changed 417 atom styles  

> hide sel surfaces

> select clear

> select /AAZ:96@CD1

1 atom, 1 residue, 1 model selected  

> select /AD:19@CG1

1 atom, 1 residue, 1 model selected  

> select add /AAZ:124@CD2

2 atoms, 2 residues, 2 models selected  

> distance /AD:19@CG1 /AAZ:124@CD2

Distance between /AD VAL 19 CG1 and /AAZ TYR 124 CD2: 129.616Å  

> close #2

> select /AAG:125@CA

1 atom, 1 residue, 1 model selected  

> select add /AAZ:109@C

2 atoms, 2 residues, 2 models selected  

> select clear

> select /AAZ:110@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select /AAZ:156@N

1 atom, 1 residue, 1 model selected  

> select add /AAG:42@CA

2 atoms, 2 residues, 1 model selected  

> distance /AAZ:156@N /AAG:42@CA

Distance between /AAZ CYS 156 N and /AAG PRO 42 CA: 130.700Å  

> close #2

> select clear

> select /AAZ:110@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select /ABA:44@O

1 atom, 1 residue, 1 model selected  

> select clear

> select /AAG:153@CB

1 atom, 1 residue, 1 model selected  

> select add /ABA:44@O

2 atoms, 2 residues, 2 models selected  

> distance /AAG:153@CB /ABA:44@O

Distance between /AAG VAL 153 CB and /ABA GLU 44 O: 126.731Å  

> save /Users/claudiabocz/Desktop/exercise_class11.cxs

> close session

> open 1OMP fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 1OMP fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 1OMP bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/1omp-assembly-1.cif.gz  
  
1OMP bioassembly 1 title:  
Crystallographic evidence of A large ligand-induced hinge-twist motion between
the two domains of the maltodextrin-binding protein involved In active
transport and chemotaxis [more info...]  
  
Chain information for 1OMP bioassembly 1 #1  
---  
Chain | Description  
A | D-MALTODEXTRIN BINDING PROTEIN  
  
Opened 1 biological assemblies for 1OMP  

> open 1ANF fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 1ANF fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 1ANF bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/1anf-assembly-1.cif.gz  
  
1ANF bioassembly 1 title:  
Maltodextrin binding protein with bound maltose [more info...]  
  
Chain information for 1ANF bioassembly 1 #2  
---  
Chain | Description  
A | MALTODEXTRIN-BINDING PROTEIN  
  
Non-standard residues in 1ANF bioassembly 1 #2  
---  
GLC — (GLC)  
  
Opened 1 biological assemblies for 1ANF  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1OMP bioassembly 1, chain A (#1) with 1ANF bioassembly 1, chain A
(#2), sequence alignment score = 1885.9  
RMSD between 202 pruned atom pairs is 0.547 angstroms; (across all 370 pairs:
7.241)  
  

> Write model #1,2, frames 40

Unknown command: Write model #1,2, frames 40  

> morph #1,2, frames 40

Missing or invalid "structures" argument: only initial part "#1,2" of atom
specifier valid  

> morph #1,2 frames 40

Computed 41 frame morph #3  

> coordset #3 1,41

> movie record

> movie stop

> movie record

> movie stop

> movie encode "/Users/claudiabocz/Desktop/HSC308 part B.mp4"

Movie saved to /Users/claudiabocz/Desktop/HSC308 part B.mp4  
  


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-20.2.48
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir9,1
      Processor Name: Dual-Core Intel Core i3
      Processor Speed: 1.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 512 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
      OS Loader Version: 564.40.4~55

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 52 days, 54 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a5c
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    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: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    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: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    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: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    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: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

[Tom Goddard]

Apple Intel graphics driver crash.