Opened 18 months ago

Closed 18 months ago

#15200 closed defect (can't reproduce)

Crash changing Mac display configuration

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
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: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000000031887f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000317873000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316867000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031585b000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031484f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000313843000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000312837000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031182b000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031081f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030f813000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030e807000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fa9f3ac0 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath (total: 53)


{"app_name":"ChimeraX","timestamp":"2024-05-14 11:48:41.00 +0200","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"CF26F3C4-D6DC-404C-956D-8E8C5CA2CB47"}
{
  "uptime" : 52000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 4270,
  "osVersion" : {
    "train" : "macOS 14.4.1",
    "build" : "23E224",
    "releaseType" : "User"
  },
  "captureTime" : "2024-05-14 11:48:25.5906 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "CF26F3C4-D6DC-404C-956D-8E8C5CA2CB47",
  "pid" : 14752,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-05-13 12:52:14.9906 +0200",
  "procStartAbsTime" : 411165318732,
  "procExitAbsTime" : 1249309274939,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"193B2E1E-DB7D-5B6D-A4AF-4578F1788E24","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3919119D-5F63-DE2E-EEA6-B7CB81FBA650",
  "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" : 11748,
  "sleepWakeUUID" : "BF5CC7A6-80D1-44C6-B47F-B3E43694926A",
  "sip" : "enabled",
  "vmRegionInfo" : "0x15808d74c is in 0x158000000-0x161e10000;  bytes after start: 579404  bytes before end: 165161139\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_MEDIUM               150000000-158000000    [128.0M] rw-\/rwx SM=PRV  \n--->  __TEXT                      158000000-161e10000    [158.1M] r-x\/rwx SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore\n      __DATA_CONST                161e10000-162450000    [ 6400K] r--\/rwx SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
  "exception" : {"codes":"0x0000000000000002, 0x000000015808d74c","rawCodes":[2,5771941708],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x000000015808d74c"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":14752},
  "vmregioninfo" : "0x15808d74c is in 0x158000000-0x161e10000;  bytes after start: 579404  bytes before end: 165161139\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_MEDIUM               150000000-158000000    [128.0M] rw-\/rwx SM=PRV  \n--->  __TEXT                      158000000-161e10000    [158.1M] r-x\/rwx SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore\n      __DATA_CONST                161e10000-162450000    [ 6400K] r--\/rwx SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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Address size fault"},"pc":{"value":6757739104,"matchesCrashFrame":1},"far":{"value":0}},"id":235184,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":39520,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":151},{"imageOffset":27680,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":152},{"imageOffset":259304,"symbol":"raise","symbolLocation":32,"imageIndex":153},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":149},{"imageOffset":17796,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":154},{"imageOffset":579464,"imageIndex":89},{"imageOffset":343320,"imageIndex":81},{"imageOffset":343160,"imageIndex":81},{"imageOffset":380320,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":155},{"imageOffset":11472316,"symbol":"-[NSWindow 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    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6757007360,
    "size" : 577528,
    "uuid" : "08c4329e-407f-310b-b037-75a8020b2963",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  }
],
  "sharedCache" : {
  "base" : 6753484800,
  "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=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG image                          2976K      152 \nColorSync                          720K       35 \nCoreAnimation                     7168K      371 \nCoreGraphics                        64K        4 \nCoreImage                          160K       10 \nCoreUI image data                 5856K       59 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             2.3G      142 \nMALLOC guard page                  384K       24 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        784K       49 \nStack                            331.8M       50 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      426.5M      335 \nVM_ALLOCATE (reserved)           128.0M        2         reserved VM address space (unallocated)\n__AUTH                            2205K      407 \n__AUTH_CONST                      31.9M      626 \n__CTF                               824        1 \n__DATA                            22.0M      772 \n__DATA_CONST                      42.6M      783 \n__DATA_DIRTY                      2030K      234 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       554.5M      152 \n__OBJC_RO                         71.7M        1 \n__OBJC_RW                         2195K        1 \n__TEXT                           937.6M      800 \ndyld private memory                320K        3 \nmapped file                      639.1M      120 \nshared memory                     3344K       36 \n===========                     =======  ======= \nTOTAL                              5.5G     5189 \nTOTAL, minus reserved VM space     5.4G     5189 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "d63c983737224f5337232ed7b7987ba50c73be43",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "63f9578e238e7b23a1f3030a",
      "factorPackIds" : {

      },
      "deploymentId" : 240000005
    },
    {
      "rolloutId" : "64c025b28b7f0e739e4fbe58",
      "factorPackIds" : {

      },
      "deploymentId" : 240000019
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "a34d22a1-a1a5-4126-a477-0c499e502c6a",
      "experimentId" : "65835bc103dc58766bab2d27",
      "deploymentId" : 400000011
    },
    {
      "treatmentId" : "5d85d104-adc7-4ebf-8b7c-96d84fdad9cc",
      "experimentId" : "6384d56b96e8d228551ec182",
      "deploymentId" : 400000032
    }
  ]
}
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Compositor returned null texture  

> open 1URJ

1urj title:  
Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1 [more
info...]  
  
Chain information for 1urj #1  
---  
Chain | Description | UniProt  
A B | MAJOR DNA-BINDING PROTEIN | DNBI_HSV11 1-1136  
  
Non-standard residues in 1urj #1  
---  
HG — mercury (II) ion  
ZN — zinc ion  
  
1urj mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui tool show "Scale Bar"

> scalebar

> scalebar 140

> close

> open /Users/pep/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close

> open /Volumes/SUN-CPR-Kummer-Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb
> format pdb

No such file/path: /Volumes/SUN-CPR-Kummer-
Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb  

> open /Volumes/SUN-CPR-Kummer-Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb
> format pdb

No such file/path: /Volumes/SUN-CPR-Kummer-
Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb  

> open /Volumes/SUN-CPR-Kummer-Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb
> format pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
B C | No description available  
  

> scalebar 140

> scalebar 124

> color bynucleotide

> scalebar off

> lighting simple

> set bgColor white

> lighting soft

> lighting flat

> lighting full

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> sequence chain /B /C

Alignment identifier is 1  

> select /B-C:1-2

36 atoms, 36 bonds, 4 residues, 1 model selected  

> select /B-C:1-534

8350 atoms, 8544 bonds, 1068 residues, 1 model selected  

> color sel #cc3333ff

> color sel #993333ff

> color sel #cc3333ff

> select clear

> select /B-C:535-536

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select /B-C:535-808

4246 atoms, 4340 bonds, 548 residues, 1 model selected  

> select
> /B-C:19-26,31-35,40-47,85-96,111-123,132-134,143-145,152-157,160-163,174-182,189-202,215-225,227-229,240-243,255-262,277-280,284-293,305-317,334-339,376-384,400-402,416-422,426-447,450-453,457-461,463-474,476-489,505-531,539-544,546-555,562-573,575-592,594-597,600-610,636-651,656-658,667-689,696-699,702-711,722-738,755-757,760-769,780-789,791-794,805-809,815-817,823-831,834-836,846-848

6896 atoms, 6940 bonds, 862 residues, 1 model selected  

> select clear

> select /B-C:535

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:535-849

4856 atoms, 4964 bonds, 630 residues, 1 model selected  

> color sel #330000ff

> color sel #ff0000ff

> color sel #ff9966ff

> color sel #990000ff

> color sel #330000ff

> select clear

> color #333333ff

> undo

> select /B-C:535

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:535-849

4856 atoms, 4964 bonds, 630 residues, 1 model selected  

> color sel #666666ff

> select clear

> select /B-C:564

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:564-573

160 atoms, 158 bonds, 20 residues, 1 model selected  

> select /B-C:565

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:565-611

766 atoms, 778 bonds, 94 residues, 1 model selected  

> select /B-C:564-565

34 atoms, 32 bonds, 4 residues, 1 model selected  

> select /B-C:564-829

4116 atoms, 4206 bonds, 532 residues, 1 model selected  

> select /B-C:564

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:564-832

4162 atoms, 4252 bonds, 538 residues, 1 model selected  

> select clear

> select /B

6603 atoms, 6755 bonds, 849 residues, 1 model selected  

> roll

> stop

> orient reset

Unknown command: orient reset  

> view orient

> select clear

> turn 90

Expected an axis vector or a keyword  

> turn 90x

Expected an axis vector or a keyword  

> turn 90 x

Expected an axis vector or a keyword  

> turn 90 90

Expected an axis vector or a keyword  

> turn x 90

> turn x -90

> turn x 180

> turn x -180

> ui tool show "Side View"

> turn z 90

> turn z -90

> turn y 90

> turn 180

Expected an axis vector or a keyword  

> turn 180

Expected an axis vector or a keyword  

> turn x 180

> undo

> view orient

> lighting flat

> lighting full

> lighting flat

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> set bgColor gray

> set bgColor white

> lighting full

> lighting simple

> show surfaces

> lighting soft

> lighting simple

> lighting full

> hide surfaces

> show cartoons

> surface style dot

> show surfaces

> select helix

6896 atoms, 6940 bonds, 862 residues, 1 model selected  

> select strand

1458 atoms, 1442 bonds, 181 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> select

13206 atoms, 13510 bonds, 1698 residues, 1 model selected  

> hide sel surfaces

> select clear

> select helix

6896 atoms, 6940 bonds, 862 residues, 1 model selected  

> select clear

> select strand

1458 atoms, 1442 bonds, 181 residues, 1 model selected  

> select clear

> select /B-C:783

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:783-792

168 atoms, 170 bonds, 20 residues, 1 model selected  

> select /B-C:773

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:773-795

384 atoms, 392 bonds, 46 residues, 1 model selected  

> select /B-C:766

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:766-795

498 atoms, 510 bonds, 60 residues, 1 model selected  

> select /B-C:760

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:760-794

576 atoms, 588 bonds, 70 residues, 1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save /Users/pep/Desktop/s format fasta alignment 1

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /B-C:1-2

36 atoms, 36 bonds, 4 residues, 1 model selected  

> select /B-C:1-654

10220 atoms, 10454 bonds, 1308 residues, 1 model selected  

> select /B-C:66

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select /B-C:66-231

2588 atoms, 2632 bonds, 332 residues, 1 model selected  

> select clear

> view orient

> turn y 90

> save /Users/pep/Desktop/image39.png supersample 3

> turn y -90

> save /Users/pep/Desktop/image40.png supersample 3

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> rainbow

> view orient

> save /Users/pep/Desktop/image41.png supersample 3

> ui tool show "AlphaFold Error Plot"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Must choose path to predicted aligned file  

> alphafold pae #1 file /Volumes/SUN-CPR-Kummer-
> Group/PepCunillSubiranas/AF_UL9/result_model_5_multimer_v3_pred_0.pkl

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color #1/B:11-547 lime

> color #1/B:18-313 lime

> color #1/B:550-849/C:1-4 magenta

> color #1/B:7-272 lime

> color #1/B:279-533 magenta

> color #1/B:537-849/C:1-11 lime

> color #1/B:537-836 lime

> color #1/C:35-258 magenta

> color #1/B:533-849 lime

> color #1/C:7-282 lime

> color #1/C:275-550 lime

> color #1/C:4-533 lime

> color #1/C:399-399 lime

> color #1/C:334-334 magenta

> color #1/C:21-533 lime

> color #1/C:557-557 lime

> color #1/C:269-269 magenta

> color #1/C:286-540 lime

> color #1/C:516-849 lime

> color #1/B:18-843 lime

> color #1/C:11-849 lime

> color #1/B:14-843 magenta

> color #1/B:11-533 lime

> color #1/C:21-530 magenta

> color #1/B:523-849/C:1-7 lime

> color #1/C:14-537 magenta

> color #1/B:447-447 lime

> color #1/C:337-337 magenta

> color #1/B:11-76 lime

> color #1/C:21-45 magenta

> color #1/B:516-843 lime

> color #1/C:11-530 magenta

> color #1/B:777-777 lime

> color #1/C:296-296 magenta

> color #1/C:7-540 lime

> color #1/C:513-513 lime

> color #1/C:636-636 magenta

> color #1/C:4-849 lime

> color #1/B:4-846 lime

> color #1/B:4-843 lime

> color #1/C:7-849 magenta

> color #1/C:11-11 lime

> color #1/C:705-705 magenta

> color #1/B:4-846 lime

> color #1/C:11-849 magenta

> color #1/C:330-330 lime

> color #1/B:674-674 magenta

> color #1/C:14-849 lime

> color #1/B:4-849 magenta

> color #1/C:654-654 lime

> color #1/B:757-757 magenta

> ui tool show "ESMFold Error Plot"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Must choose path to predicted aligned file  

> esmfold pae #1 file /Volumes/SUN-CPR-Kummer-
> Group/PepCunillSubiranas/AF_UL9/result_model_5_multimer_v3_pred_0.pkl

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color #1/C:21-303 lime

> color #1/C:38-547 lime

> color #1/C:14-265 lime

> color #1/C:293-293 lime

> color #1/C:300-300 magenta

> color #1/C:7-605 lime

> color #1/C:526-526 lime

> color #1/C:379-379 magenta

> color #1/C:7-279 lime

> color #1/C:540-540 lime

> color #1/C:372-375 magenta

> color #1/C:25-547 lime

> color #1/C:327-327 lime

> color #1/C:547-547 magenta

> color #1/C:265-537 lime

> color #1/C:523-523 lime

> color #1/C:585-585 magenta

> color #1/C:533-843 lime

> color #1/C:471-471 lime

> color #1/C:341-341 magenta

> color #1/B:21-547 lime

> color #1/B:657-657 lime

> color #1/B:296-296 magenta

> color #1/B:557-832 lime

> color #1/B:21-286 magenta

> color #1/C:561-561 lime

> color #1/B:825-825 magenta

> undo

>

Incomplete command: shape  

> shape cylinder

> select

13206 atoms, 13510 bonds, 1698 residues, 2 models selected  

> shape cylinder

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> PipesAndPlanks

Unknown command: PipesAndPlanks  

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> select clear

> cartoon style xsection oval modeHelix default

> undo

> ui tool show "Basic Actions"

> hide /B target abp

> ui tool show "Render by Attribute"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

> undo

> view orient

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette

> color byattribute bfactor palette

Missing "palette" keyword's argument  

> color bfactor palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> view orient

> lighting soft

> lighting simple

> lighting soft

> lighting full

> undo

> ui tool show "Surface Color"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show "Color Key"

> ui mousemode right "color key"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key blue-white-red :min : :max white:

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key blue:min white: red:max white: white:

> key white: white: red:max white: blue:min

> key blue:min white: red:max white: white:

> key white: white: red:max white: blue:min

> key white: white: red:max white: blue:1

> key white: white: red:max white: blue:10

> key white: white: red:max white: blue:100

> key white: white: red:max white:9 blue:100

> key white: white: red:max white:90 blue:100

> key white: white: red:7 white:90 blue:100

> key white: white: red:70 white:90 blue:100

> key white: white:5 red:70 white:90 blue:100

> key white: white:50 red:70 white:90 blue:100

> key white:0 white:50 red:70 white:90 blue:100

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key numericLabelSpacing equal

> key white:0 white:50 red:70 #f8fffa:90 blue:100

> key white:0 white:50 red:70 #f9fffb:90 blue:100

> key white:0 white:50 red:70 #f8fffb:90 blue:100

> key white:0 white:50 red:70 #f8fffc:90 blue:100

> key white:0 white:50 red:70 #f7fffc:90 blue:100

> key white:0 white:50 red:70 #f6fffc:90 blue:100

> key white:0 white:50 red:70 #f3fffd:90 blue:100

> key white:0 white:50 red:70 #f1fffe:90 blue:100

> key white:0 white:50 red:70 #f0fffe:90 blue:100

> key white:0 white:50 red:70 #eaffff:90 blue:100

> key white:0 white:50 red:70 #e6feff:90 blue:100

> key white:0 white:50 red:70 #dffdff:90 blue:100

> key white:0 white:50 red:70 #d9fbff:90 blue:100

> key white:0 white:50 red:70 #d6faff:90 blue:100

> key white:0 white:50 red:70 #d2f9ff:90 blue:100

> key white:0 white:50 red:70 #cbf7ff:90 blue:100

> key white:0 white:50 red:70 #caf6ff:90 blue:100

> key white:0 white:50 red:70 #c5f5ff:90 blue:100

> key white:0 white:50 red:70 #bff2ff:90 blue:100

> key white:0 white:50 red:70 #bcf1ff:90 blue:100

> key white:0 white:50 red:70 #baf0ff:90 blue:100

> key white:0 white:50 red:70 #b5edff:90 blue:100

> key white:0 white:50 red:70 #b3ecff:90 blue:100

> key white:0 white:50 red:70 #b2ebff:90 blue:100

> key white:0 white:50 red:70 #afeaff:90 blue:100

> key white:0 white:50 red:70 #aee9ff:90 blue:100

> key white:0 white:50 red:70 #ade8ff:90 blue:100

> key white:0 white:50 red:70 #aae6ff:90 blue:100

> key white:0 white:50 red:70 #a9e5ff:90 blue:100

> key white:0 white:50 red:70 #a7e5ff:90 blue:100

> key white:0 white:50 red:70 #a5e3ff:90 blue:100

> key white:0 white:50 red:70 #a5e2ff:90 blue:100

> key white:0 white:50 red:70 #a4e2ff:90 blue:100

> key white:0 white:50 red:70 #a2e1ff:90 blue:100

> key white:0 white:50 red:70 #a1e0ff:90 blue:100

> key white:0 white:50 red:70 #a0e0ff:90 blue:100

> key white:0 white:50 red:70 #a0dfff:90 blue:100

> key white:0 white:50 red:70 #9fdfff:90 blue:100

> key white:0 white:50 red:70 #9dddff:90 blue:100

> key white:0 white:50 red:70 #9bddff:90 blue:100

> key white:0 white:50 red:70 #9bdcff:90 blue:100

> key white:0 white:50 red:70 #9adcff:90 blue:100

> key white:0 white:50 red:70 #9adbff:90 blue:100

> key white:0 white:50 red:70 #99dbff:90 blue:100

> key white:0 white:50 red:70 #97daff:90 blue:100

> key white:0 white:50 red:70 #96d9ff:90 blue:100

> key white:0 white:50 red:70 #95d9ff:90 blue:100

> key white:0 white:50 red:70 #94d8ff:90 blue:100

> key white:0 white:50 red:70 #92d8ff:90 blue:100

> key white:0 white:50 red:70 #91d7ff:90 blue:100

> key white:0 white:50 red:70 #8fd7ff:90 blue:100

> key white:0 white:50 red:70 #8ed6ff:90 blue:100

> key white:0 white:50 red:70 #8dd6ff:90 blue:100

> key white:0 white:50 red:70 #8cd6ff:90 blue:100

> key white:0 white:50 red:70 #8bd5ff:90 blue:100

> key white:0 white:50 red:70 #8ad4ff:90 blue:100

> key white:0 white:50 red:70 #88d4ff:90 blue:100

> key white:0 white:50 red:70 #87d3ff:90 blue:100

> key white:0 white:50 red:70 #85d3ff:90 blue:100

> key white:0 white:50 red:70 #82d2ff:90 blue:100

> key white:0 white:50 red:70 #81d1ff:90 blue:100

> key white:0 white:50 red:70 #80d1ff:90 blue:100

> key white:0 white:50 red:70 #7fd1ff:90 blue:100

> key white:0 white:50 red:70 #7ed0ff:90 blue:100

> key white:0 white:50 red:70 #7ccfff:90 blue:100

> key white:0 white:50 red:70 #7aceff:90 blue:100

> key white:0 white:50 red:70 #79ceff:90 blue:100

> key white:0 white:50 red:70 #79cdff:90 blue:100

> key white:0 white:50 red:70 #78cdff:90 blue:100

> key white:0 white:50 red:70 #77cdff:90 blue:100

> key white:0 white:50 red:70 #76ccff:90 blue:100

> key white:0 white:50 red:70 #76cbff:90 blue:100

> key white:0 white:50 red:70 #75cbff:90 blue:100

> key white:0 white:50 red:70 #74cbff:90 blue:100

> key white:0 white:50 red:70 #74caff:90 blue:100

> key white:0 white:50 red:70 #73caff:90 blue:100

> key white:0 white:50 red:70 #70c8ff:90 blue:100

> key white:0 white:50 red:70 #6fc8ff:90 blue:100

> key white:0 white:50 red:70 #6dc7ff:90 blue:100

> key white:0 white:50 red:70 #69c5ff:90 blue:100

> key white:0 white:50 red:70 #66c4ff:90 blue:100

> key white:0 white:50 red:70 #64c2ff:90 blue:100

> key white:0 white:50 red:70 #63c2ff:90 blue:100

> key white:0 white:50 red:70 #61c1ff:90 blue:100

> key white:0 white:50 red:70 #60c0ff:90 blue:100

> key white:0 white:50 red:70 #5ebfff:90 blue:100

> key white:0 white:50 red:70 #5cbfff:90 blue:100

> key white:0 white:50 red:70 #5bbeff:90 blue:100

> key white:0 white:50 red:70 #5abeff:90 blue:100

> key white:0 white:50 red:70 #58bcff:90 blue:100

> key white:0 white:50 red:70 #57bcff:90 blue:100

> key white:0 white:50 red:70 #56bbff:90 blue:100

> key white:0 white:50 red:70 #55bbff:90 blue:100

> key white:0 white:50 red:70 #53bbff:90 blue:100

> key white:0 white:50 red:70 #51baff:90 blue:100

> key white:0 white:50 red:70 #50b9ff:90 blue:100

> key white:0 white:50 red:70 #4eb8ff:90 blue:100

> key white:0 white:50 red:70 #4cb7ff:90 blue:100

> key white:0 white:50 red:70 #4ab6ff:90 blue:100

> key white:0 white:50 red:70 #48b6ff:90 blue:100

> key white:0 white:50 red:70 #48b5ff:90 blue:100

> key white:0 white:50 red:70 #46b4ff:90 blue:100

> key white:0 white:50 red:70 #44b3ff:90 blue:100

> key white:0 white:50 red:70 #43b2ff:90 blue:100

> key white:0 white:50 red:70 #41b1ff:90 blue:100

> key white:0 white:50 red:70 #3fb0ff:90 blue:100

> key white:0 white:50 red:70 #3caeff:90 blue:100

> key white:0 white:50 red:70 #3cadff:90 blue:100

> key white:0 white:50 red:70 #38abff:90 blue:100

> key white:0 white:50 red:70 #37aaff:90 blue:100

> key white:0 white:50 red:70 #37a9ff:90 blue:100

> key white:0 white:50 red:70 #35a8ff:90 blue:100

> key white:0 white:50 red:70 #32a6ff:90 blue:100

> key white:0 white:50 red:70 #30a4ff:90 blue:100

> key white:0 white:50 red:70 #30a3ff:90 blue:100

> key white:0 white:50 red:70 #2fa3ff:90 blue:100

> key white:0 white:50 red:70 #2ea2ff:90 blue:100

> key white:0 white:50 red:70 #2da1ff:90 blue:100

> key white:0 white:50 red:70 #2ca1ff:90 blue:100

> key white:0 white:50 red:70 #2ca0ff:90 blue:100

> key white:0 white:50 red:70 #2ba0ff:90 blue:100

> key white:0 white:50 red:70 #2b9fff:90 blue:100

> key white:0 white:50 red:70 #2a9fff:90 blue:100

> key white:0 white:50 red:70 #2a9eff:90 blue:100

> key white:0 white:50 red:70 #299eff:90 blue:100

> key white:0 white:50 red:70 #299dff:90 blue:100

> key white:0 white:50 red:70 #289eff:90 blue:100

> key white:0 white:50 red:70 #299dff:90 blue:100

> key white:0 white:50 red:70 #2a9dff:90 blue:100

> key white:0 white:50 red:70 #2b9dff:90 blue:100

> key white:0 white:50 red:70 #2c9eff:90 blue:100

> key white:0 white:50 red:70 #2e9fff:90 blue:100

> key white:0 white:50 red:70 #2fa0ff:90 blue:100

> key white:0 white:50 red:70 #30a0ff:90 blue:100

> key white:0 white:50 red:70 #35a5ff:90 blue:100

> key white:0 white:50 red:70 #37a7ff:90 blue:100

> key white:0 white:50 red:70 #38a8ff:90 blue:100

> key white:0 white:50 red:70 #3cacff:90 blue:100

> key white:0 white:50 red:70 #3dadff:90 blue:100

> key white:0 white:50 red:70 #3daeff:90 blue:100

> key white:0 white:50 red:70 #3fb1ff:90 blue:100

> key white:0 white:50 red:70 #41b4ff:90 blue:100

> key white:0 white:50 red:70 #42b7ff:90 blue:100

> key white:0 white:50 red:70 #43b9ff:90 blue:100

> key white:0 white:50 red:70 #44bcff:90 blue:100

> key white:0 white:50 red:70 #44bdff:90 blue:100

> key white:0 white:50 red:70 #45bfff:90 blue:100

> key white:0 white:50 red:70 #46c1ff:90 blue:100

> key white:0 white:50 red:70 #47c5ff:90 blue:100

> key white:0 white:50 red:70 #48c7ff:90 blue:100

> key white:0 white:50 red:70 #49cbff:90 blue:100

> key white:0 white:50 red:70 #4acdff:90 blue:100

> key white:0 white:50 red:70 #4aceff:90 blue:100

> key white:0 white:50 red:70 #4acfff:90 blue:100

> key white:0 white:50 red:70 #4ad0ff:90 blue:100

> key white:0 white:50 red:70 #4bd1ff:90 blue:100

> key white:0 white:50 red:70 #4bd2ff:90 blue:100

> key white:0 white:50 red:70 #4bd3ff:90 blue:100

> key white:0 white:50 red:70 #4cd4ff:90 blue:100

> key white:0 white:50 red:70 #4cd5ff:90 blue:100

> key white:0 white:50 red:70 #4cd6ff:90 blue:100

> key white:0 white:50 red:70 #4dd7ff:90 blue:100

> key white:0 white:50 red:70 #4dd8ff:90 blue:100

> key white:0 white:50 red:70 #4ed9ff:90 blue:100

> key white:0 white:50 red:70 #4dd9ff:90 blue:100

> key white:0 white:50 red:70 #4cdaff:90 blue:100

> key white:0 white:50 red:70 #4cdbff:90 blue:100

> key white:0 white:50 red:70 #4cdcff:90 blue:100

> key white:0 white:50 red:70 #4bddff:90 blue:100

> key white:0 white:50 red:70 #4adeff:90 blue:100

> key white:0 white:50 red:70 #4adfff:90 blue:100

> key white:0 white:50 red:70 #49dfff:90 blue:100

> key white:0 white:50 red:70 #48dfff:90 blue:100

> key white:0 white:50 red:70 #47e0ff:90 blue:100

> key white:0 white:50 red:70 #46e0ff:90 blue:100

> color key alphafold

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> 2dlabels

> key labelColor #bfbfbf

> key labelColor default

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 21

> key fontSize 22

> key fontSize 23

> key fontSize 24

> key fontSize 25

> key fontSize 26

> key fontSize 27

> key fontSize 28

> key fontSize 29

> key fontSize 30

> key fontSize 31

> key fontSize 32

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key alphafold :0 :50 :70 :90 :100

> key pos 0.768809,0.116257 size 0.00882056,0.0013392

> key pos 0.782114,0.06833 size 0.204062,0.123147

> key pos 0.698122,0.0823282 size 0,0

> key pos 0.658725,0.1046 size 0.313036,0.0376553

> undo

> key pos 0.604018,0.0666726

> key fontSize 31

> key pos 0.636059,0.102636 size 0.27705,0.0392079

> key paecontacts :100 :90 :70 :50 :0

> key alphafold :0 :50 :70 :90 :100

> undo

> key pos 0.637544,0.0996112

> ui mousemode right translate

> ui mousemode left 'color key'

> ui mousemode left rotate

> ui mousemode right 'color key'

> help help:user/tools/colorkey.html

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> 2dlabels text "pLDDT values"

> key pos 0.168664,0.471023 size 0.361155,0.0398326

> key pos 0.539279,0.0803392

> key pos 0.527306,0.435428 size 0.00759199,0.0740672

> undo

> key pos 0.656943,0.0565185 size 0.273768,0.0225437

> key pos 0.548738,0.430832 size 0.2568,0.077924

> key pos 0.575605,0.0834756 size 0.360068,0.0221138

> ui mousemode right translate

> ui mousemode right "move label"

> 2dlabels #6.1 xpos 0.579 ypos 0.120

> 2dlabels #6.1 xpos 0.672 ypos 0.175

> ui mousemode right "color key"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key pos 0.591624,0.141009 size 0.152361,0.0260973

> key pos 0.56595,0.0847163

> ui mousemode right "move label"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui mousemode right "move label"

> 2dlabels #6.2 xpos 1.231 ypos 0.363

> 2dlabels #6.1 xpos 0.566 ypos 0.120

> view orient

> hide cartoons

> show cartoons

> color bfactor #1 palette esmfold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor #1 palette esmfold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor #1 palette esmfold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> save /Users/pep/Desktop/image42.png supersample 3

> turn x 90

> turn y 90

> save /Users/pep/Desktop/image43.png supersample 3

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> select /B-C:231-232

34 atoms, 34 bonds, 4 residues, 1 model selected  

> select /B-C:1-232

3586 atoms, 3658 bonds, 464 residues, 1 model selected  

> select /B

6603 atoms, 6755 bonds, 849 residues, 1 model selected  

> view orient

> turn y 90

> axis

Unknown command: axis  

> select clear

> select /B-C:1

22 atoms, 22 bonds, 2 residues, 1 model selected  

> select /B-C:1-19

248 atoms, 252 bonds, 38 residues, 1 model selected  

> select /B-C:544

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:544-549

90 atoms, 88 bonds, 12 residues, 1 model selected  

> select
> /B-C:19-26,31-35,40-47,85-96,111-123,132-134,143-145,152-157,160-163,174-182,189-202,215-225,227-229,240-243,255-262,277-280,284-293,305-317,334-339,376-384,400-402,416-422,426-447,450-453,457-461,463-474,476-489,505-531,539-544,546-555,562-573,575-592,594-597,600-610,636-651,656-658,667-689,696-699,702-711,722-738,755-757,760-769,780-789,791-794,805-809,815-817,823-831,834-836,846-848

6896 atoms, 6940 bonds, 862 residues, 1 model selected  

> select clear

> select /B-C:544

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:539-544

80 atoms, 80 bonds, 12 residues, 1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /B-C:623

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:623-629

108 atoms, 106 bonds, 14 residues, 1 model selected  

> select /B-C:539

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:539-544

80 atoms, 80 bonds, 12 residues, 1 model selected  

> select /B-C:539-544,624-629

170 atoms, 168 bonds, 24 residues, 1 model selected  

> show sel atoms

> select clear

> undo

> color (#!1 & sel) red

> select clear

> select /B

6603 atoms, 6755 bonds, 849 residues, 1 model selected  

> select clear

> color bfactor

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Already setting window visible!  

> alphafold pae #1 colorDomains true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color bfactor #1 palette esmfold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor #1 palette esmfold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Already setting window visible!  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> help help:user/tools/alphafold.html#pae

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color #1/B:1-1 lime

> color #1/B:3-849/C:1-849 lime

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> help help:user/tools/alphafold.html#pae

> axiscolor plot alphafold

Unknown command: axiscolor plot alphafold  

> color plot alphafold

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show "Color Actions"

> key pae :0 : : :15 : : :30 showTool true

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> ui tool show "Side View"

> key paegreen :0 : : :15 : : :30 showTool true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color paegreen

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> key red:low orange: yellow: cornflowerblue: blue:high

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

Already setting window visible!  

> select
> /B-C:19-26,31-35,40-47,85-96,111-123,132-134,143-145,152-157,160-163,174-182,189-202,215-225,227-229,240-243,255-262,277-280,284-293,305-317,334-339,376-384,400-402,416-422,426-447,450-453,457-461,463-474,476-489,505-531,539-544,546-555,562-573,575-592,594-597,600-610,636-651,656-658,667-689,696-699,702-711,722-738,755-757,760-769,780-789,791-794,805-809,815-817,823-831,834-836,846-848

6896 atoms, 6940 bonds, 862 residues, 1 model selected  

> color bfactor #1 palette paegreen

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> select clear

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key paegreen :0 : : :15 : : :30 showTool true

> ui mousemode right "color key"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key pos 0.604378,0.134006 size 0.100855,0.0970887

> key pos 0.820187,0.123753 size 0.125421,0.0236736

> key pos 0.852465,0.226314 size 0.0136468,0.46242

> key pos 0.71884,0.101136 size 0.0230012,0.286266

> key pos 0.707525,0.0439381 size 0.241037,0.0149871

> save /Users/pep/Desktop/image44.png supersample 3

> key pos 0.14223,0.658284 size 0.279099,0.0285492

> save /Users/pep/Desktop/image45.png supersample 3

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color #1/C:524-524 lime

> color #1/C:594-594 magenta

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color #1/C:630-630 lime

> color #1/B:671-671 magenta

> alphafold pae #1 colorDomains true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key pos 0.757436,0.542016 size 0.0591203,0.0337354

> key pos 0.327701,0.687724 size 0,0

Already setting window visible!  

> color #1/C:690-690 lime

> color #1/C:152-152 magenta

> color #1/C:557-557 lime

> color #1/B:254-254 magenta

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> alphafold pae #1 colorDomains true

> lighting simple

> lighting flat

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting flat

> graphics silhouettes false

> lighting soft

> lighting full

> lighting flat

> lighting simple

> graphics silhouettes false

> color #1/C:636-636 lime

> color #1/C:284-284 magenta

> color bfactor #1 palette alphafold

13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1  

> key pos 0.424738,0.596559 size 0.0251048,0.0302724

> key pos 0.722385,0.526184 size 0.204108,0.121798

> key pos 0.910091,0.424162 size 0,0

> key pos 0.56261,0.102205 size 0.305485,0.0158445

> key pos 0.244068,0.094711 size 0.446295,0.0456157

> key pos 0.23177,0.0820312 size 0.437232,0.042045

> key pos 0.228959,0.0748773

> key alphafold :0 : : :50 : : :70 : : :90:::100 showTool true

Expected a keyword  

> key alphafold :0 : : :50 : : :70 : : :90:::100 showTool true

Expected a keyword  

> key alphafold :0 : : :50 : : :70 : : :90:::100 showTool true

Expected a keyword  

> key red:low orange: yellow: cornflowerblue: blue:high

> ui tool show "Color Key"

> key alphafold :low : : : :1

> key alphafold :low : : : :10

> key alphafold :low : : : :100

> key alphafold :low : : :9 :100

> key alphafold :low : : :90 :100

> key alphafold :low : :7 :90 :100

> key alphafold :low : :70 :90 :100

> key alphafold :low :5 :70 :90 :100

> key alphafold :low :50 :70 :90 :100

> key alphafold :0 :50 :70 :90 :100

> ui mousemode right "move label"

> close #4

> close #3

> view orient

> select

13206 atoms, 13510 bonds, 1698 residues, 5 models selected  

> hide sel atoms

> select clear

> save /Users/pep/Desktop/image46.png supersample 3


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

Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: Z15G0007QDK/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 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: 1 day, 17 hours, 11 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LEN T27q-20:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403220040
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (2)

comment:1 by Eric Pettersen, 18 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash changing Mac display configuration

comment:2 by Eric Pettersen, 18 months ago

Resolution: → can't reproduce
Status: assigned → closed
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