Opened 19 months ago

Closed 19 months ago

#14952 closed defect (duplicate)

Crash in garbage collection

Reported by: yakonfire@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 0x000000035dce3000 (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 0x000000035bcd7000 (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 0x000000030805b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000030704f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x0000000306043000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x0000000305037000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000030402b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000030301f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x0000000302013000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x0000000301007000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000017f3d3000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000017e3c7000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000017d3bb000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000017c3af000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000017b3a3000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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/chimerax/atomic/molarray.py", line 161 in 
  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__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 774 in _find_acceptors
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 498 in find_hbonds
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/cmd.py", line 94 in cmd_hbonds
  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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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: 57)


{"app_name":"ChimeraX","timestamp":"2024-04-10 23:59:58.00 -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":"CF6798E0-45D8-4375-A0D4-A125BC4F783D"}
{
  "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" : "2024-04-10 23:59:56.2608 -0600",
  "codeSigningMonitor" : 1,
  "incident" : "CF6798E0-45D8-4375-A0D4-A125BC4F783D",
  "pid" : 34026,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-04-10 23:44:07.4546 -0600",
  "procStartAbsTime" : 6185371561954,
  "procExitAbsTime" : 6208141820974,
  "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" : 2569,
  "sleepWakeUUID" : "1E2D91F6-0AFE-439C-9DD3-DDA48B79E181",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 4298309463\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100330000-100334000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":34026},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 4298309463\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100330000-100334000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
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    "size" : 2899968,
    "uuid" : "c315e2a3-3fd1-3a2b-b205-b8b492b0f506",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6834044928,
    "size" : 559580,
    "uuid" : "f6dd3ec2-85a4-3ab1-8486-b189cd980ebe",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6838173696,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5083136,
    "uuid" : "33908a83-098f-3437-973e-fb848c4f39df",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "2420"
  }
],
  "sharedCache" : {
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  "size" : 4189880320,
  "uuid" : "a53b7d2f-a773-3524-8828-248b33ef0b4e"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           176K        9 \nColorSync                          624K       29 \nCoreAnimation                     2176K       90 \nCoreGraphics                        32K        2 \nCoreUI image data                 4064K       29 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             2.8G      130 \nMALLOC guard page                  384K       24 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        640K       40 \nStack                            389.0M       41 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      465.2M      362 \n__AUTH                            2787K      414 \n__AUTH_CONST                      32.7M      632 \n__CTF                               824        1 \n__DATA                            25.4M      776 \n__DATA_CONST                      42.5M      789 \n__DATA_DIRTY                      1878K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       555.3M      152 \n__OBJC_RO                         71.7M        1 \n__OBJC_RW                         2195K        1 \n__TEXT                           961.5M      806 \ndyld private memory                464K        4 \nmapped file                      210.7M       53 \nshared memory                     4000K       45 \n===========                     =======  ======= \nTOTAL                              5.5G     4673 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "ca100c34a56764d7856ee9dcb1431caef0850939",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "64b21a7351cbb02ce3442e4e",
      "factorPackIds" : {
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}
}
===== Log before crash start =====
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 AA8

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AA8/best_model.pdb"

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
Alignment identifier is 1/A  
Chains must have same sequence  

> 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 AB113

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB113/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/AB113/AB113_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB113/AB113_contacts_hbonds_rot.mp4  
  
Changed 2317 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB113/AB113_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB113/AB113_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, -15.69, mean
-1.94, maximum 9.57  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -8.14, mean
5.23, maximum 20.56  

> 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/AB113/AB113_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB113/AB113_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28.38, mean
-5.099, maximum 21.64  
Map values for surface "best_model.pdb_B SES surface": minimum -28.68, mean
-1.764, maximum 23.74  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB113/AB113_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB113/AB113_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB114

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB114/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/AB114/AB114_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB114/AB114_contacts_hbonds_rot.mp4  
  
Changed 2621 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB114/AB114_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB114/AB114_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, -13.42, mean
-2.04, maximum 8.95  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -10.21, mean
-0.30, maximum 11.98  

> 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/AB114/AB114_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB114/AB114_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -27.53, mean
-5.209, maximum 22.04  
Map values for surface "best_model.pdb_B SES surface": minimum -28.02, mean
-4.37, 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/AB114/AB114_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB114/AB114_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB115

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB115/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/AB115/AB115_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB115/AB115_contacts_hbonds_rot.mp4  
  
Changed 2997 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB115/AB115_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB115/AB115_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, -12.92, mean
-2.01, maximum 9.10  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.64, mean
0.07, maximum 15.16  

> 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/AB115/AB115_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB115/AB115_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -31.01, mean
-5.163, maximum 22.86  
Map values for surface "best_model.pdb_B SES surface": minimum -28.11, mean
-3.676, maximum 27.59  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB115/AB115_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB115/AB115_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB116

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB116/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/AB116/AB116_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB116/AB116_contacts_hbonds_rot.mp4  
  
Changed 2993 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB116/AB116_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB116/AB116_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, -26.30, mean
-2.14, maximum 8.77  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.64, mean
-1.14, maximum 13.60  

> 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/AB116/AB116_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB116/AB116_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28.21, mean
-4.984, maximum 22.28  
Map values for surface "best_model.pdb_B SES surface": minimum -24.38, mean
-0.4115, maximum 22.8  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB116/AB116_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB116/AB116_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB117

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB117/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/AB117/AB117_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB117/AB117_contacts_hbonds_rot.mp4  
  
Changed 3218 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB117/AB117_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB117/AB117_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, -16.36, mean
-2.02, maximum 9.00  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -10.37, mean
0.31, maximum 11.04  

> 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/AB117/AB117_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB117/AB117_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28, mean
-5.176, maximum 22.71  
Map values for surface "best_model.pdb_B SES surface": minimum -25.82, mean
-3.603, maximum 24.52  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB117/AB117_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB117/AB117_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB118

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB118/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/AB118/AB118_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB118/AB118_contacts_hbonds_rot.mp4  
  
Changed 3462 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB118/AB118_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB118/AB118_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, -20.02, mean
-2.10, maximum 9.12  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -25.51, mean
-1.41, maximum 14.20  

> 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/AB118/AB118_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB118/AB118_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -31.37, mean
-5.162, maximum 22.1  
Map values for surface "best_model.pdb_B SES surface": minimum -26.55, mean
-2.02, maximum 26.96  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB118/AB118_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB118/AB118_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB119

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB119/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/AB119/AB119_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB119/AB119_contacts_hbonds_rot.mp4  
  
Changed 3485 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB119/AB119_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB119/AB119_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, -13.53, mean
-2.21, maximum 8.67  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.04, mean
-1.15, maximum 12.17  

> 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/AB119/AB119_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB119/AB119_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -27.58, mean
-4.995, maximum 22.49  
Map values for surface "best_model.pdb_B SES surface": minimum -28.07, mean
-4.346, maximum 23.92  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB119/AB119_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB119/AB119_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB120

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB120/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/AB120/AB120_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB120/AB120_contacts_hbonds_rot.mp4  
  
Changed 3512 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB120/AB120_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB120/AB120_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, -14.41, mean
-2.20, maximum 8.84  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.88, mean
-2.71, maximum 13.48  

> 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/AB120/AB120_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB120/AB120_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28.62, mean
-5.044, maximum 22.14  
Map values for surface "best_model.pdb_B SES surface": minimum -27.88, mean
-3.932, 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/AB120/AB120_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB120/AB120_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB121

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB121/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/AB121/AB121_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB121/AB121_contacts_hbonds_rot.mp4  
  
Changed 4112 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB121/AB121_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB121/AB121_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, -16.91, mean
-2.49, maximum 9.85  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.65, mean
-1.59, maximum 21.71  

> 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/AB121/AB121_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB121/AB121_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -31.17, mean
-5.181, maximum 22.18  
Map values for surface "best_model.pdb_B SES surface": minimum -26.34, mean
-0.3724, maximum 25.4  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB121/AB121_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB121/AB121_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB122

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB122/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/AB122/AB122_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB122/AB122_contacts_hbonds_rot.mp4  
  
Changed 4310 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB122/AB122_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB122/AB122_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, -17.77, mean
-2.18, maximum 9.20  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.20, mean
-0.36, maximum 11.70  

> 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/AB122/AB122_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB122/AB122_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -27.57, mean
-5.283, maximum 21.72  
Map values for surface "best_model.pdb_B SES surface": minimum -27.5, mean
-4.797, maximum 24.21  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB122/AB122_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB122/AB122_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB124

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB124/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  
7 hydrogen bonds found  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB124/AB124_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB124/AB124_contacts_hbonds_rot.mp4  
  
Changed 4588 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB124/AB124_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB124/AB124_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, -13.45, mean
-2.46, maximum 9.59  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.47, mean
-2.37, maximum 11.53  

> 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/AB124/AB124_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB124/AB124_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -34.02, mean
-5.431, maximum 25.01  
Map values for surface "best_model.pdb_B SES surface": minimum -31.17, mean
-5.839, maximum 21.98  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB124/AB124_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB124/AB124_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB125

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB125/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/AB125/AB125_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB125/AB125_contacts_hbonds_rot.mp4  
  
Changed 4549 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB125/AB125_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB125/AB125_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, -13.83, mean
-1.95, maximum 9.51  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -19.51, mean
-1.19, maximum 14.62  

> 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/AB125/AB125_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB125/AB125_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28.59, mean
-5.134, maximum 21.93  
Map values for surface "best_model.pdb_B SES surface": minimum -30.83, mean
-4.514, maximum 28.65  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB125/AB125_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB125/AB125_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB126

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB126/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/AB126/AB126_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB126/AB126_contacts_hbonds_rot.mp4  
  
Changed 4983 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB126/AB126_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB126/AB126_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, -19.04, mean
-2.02, maximum 8.94  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.06, mean
-0.10, maximum 12.92  

> 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/AB126/AB126_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB126/AB126_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28.42, mean
-5.213, maximum 22.14  
Map values for surface "best_model.pdb_B SES surface": minimum -29.24, mean
-4.161, maximum 23.24  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB126/AB126_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB126/AB126_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB127

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB127/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/AB127/AB127_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB127/AB127_contacts_hbonds_rot.mp4  
  
Changed 5104 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB127/AB127_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB127/AB127_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, -14.24, mean
-2.41, maximum 10.34  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.51, mean
-1.48, maximum 14.40  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB127/AB127_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB127/AB127_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -32.05, mean
-5.253, maximum 22.23  
Map values for surface "best_model.pdb_B SES surface": minimum -28.54, mean
-5.662, maximum 26.73  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB127/AB127_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB127/AB127_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB129

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB129/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/AB129/AB129_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB129/AB129_contacts_hbonds_rot.mp4  
  
Changed 5621 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB129/AB129_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB129/AB129_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, -19.85, mean
-2.68, maximum 10.53  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.87, mean
-1.19, maximum 17.90  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB129/AB129_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB129/AB129_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -29.39, mean
-5.155, maximum 22.67  
Map values for surface "best_model.pdb_B SES surface": minimum -29.04, mean
-5.714, maximum 22.66  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB129/AB129_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB129/AB129_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB130

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB130/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/AB130/AB130_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB130/AB130_contacts_hbonds_rot.mp4  
  
Changed 5464 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB130/AB130_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB130/AB130_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, -17.31, mean
-2.10, maximum 8.94  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.59, mean
1.58, maximum 17.64  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB130/AB130_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB130/AB130_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -27.85, mean
-5.173, maximum 21.61  
Map values for surface "best_model.pdb_B SES surface": minimum -29.79, mean
-5.876, maximum 23.83  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB130/AB130_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB130/AB130_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB131

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB131/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  
15 hydrogen bonds found  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB131/AB131_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB131/AB131_contacts_hbonds_rot.mp4  
  
Changed 5433 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB131/AB131_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB131/AB131_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, -13.76, mean
-2.18, maximum 8.19  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.98, mean
0.29, maximum 12.85  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB131/AB131_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB131/AB131_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -34.51, mean
-5.431, maximum 26.59  
Map values for surface "best_model.pdb_B SES surface": minimum -28.09, mean
-3.165, maximum 25.44  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB131/AB131_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB131/AB131_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB132

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB132/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/AB132/AB132_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB132/AB132_contacts_hbonds_rot.mp4  
  
Changed 5471 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB132/AB132_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB132/AB132_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, -16.88, mean
-2.34, maximum 10.02  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.80, mean
0.21, maximum 12.88  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB132/AB132_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB132/AB132_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -29.23, mean
-5.169, maximum 21.76  
Map values for surface "best_model.pdb_B SES surface": minimum -30.93, mean
-5.583, maximum 25.33  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB132/AB132_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB132/AB132_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB133

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB133/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/AB133/AB133_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB133/AB133_contacts_hbonds_rot.mp4  
  
Changed 5749 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB133/AB133_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB133/AB133_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, -14.06, mean
-2.09, maximum 8.81  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -18.93, mean
-1.62, maximum 13.72  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB133/AB133_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB133/AB133_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -28.87, mean
-5.276, maximum 22.18  
Map values for surface "best_model.pdb_B SES surface": minimum -27.78, mean
-2.671, maximum 23.88  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB133/AB133_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB133/AB133_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB134

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB134/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  
7 hydrogen bonds found  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB134/AB134_contacts_hbonds.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB134/AB134_contacts_hbonds_rot.mp4  
  
Changed 5784 atom styles  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB134/AB134_sphere.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB134/AB134_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, -14.07, mean
-2.33, maximum 8.61  
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.83, mean
-1.05, maximum 15.25  

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

> ui mousemode right "color key"

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB134/AB134_coulombic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB134/AB134_coulombic_rot.mp4  
  
Changed 0 atom styles  
Map values for surface "best_model.pdb_A SES surface": minimum -30.61, mean
-5.304, maximum 22.33  
Map values for surface "best_model.pdb_B SES surface": minimum -29.18, mean
-2.281, maximum 25.18  

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

> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/AB134/AB134_hydrophobic.jpg"
> supersample 2

Movie saved to /Users/neyrinck/.../AB134/AB134_hydrophobic_rot.mp4  
  

> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults AB136

Window position QRect(1674,1188 100x30) outside any known screen, using
primary screen  

> ui mousemode right translate

> 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  


===== 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, 12 hours, 41 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

Change History (2)

comment:1 by pett, 19 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by pett, 19 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Mark,

Thanks for reporting this problem. We believe it is fixed in the current daily build, so if you use that then you shouldn't run into this kind of crash again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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