Opened 4 months ago

Closed 4 months ago

#18056 closed defect (duplicate)

Crash on Mac waking from sleep

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-15.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000003217cf000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003207cc000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031f7c9000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031e7c6000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d7c3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c7c0000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b7bd000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a7ba000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003197b7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003187b4000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003177b1000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003167ae000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003157ab000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000202aa8200 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-06-23 07:09:56.00 -0500","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"69AE04A8-7040-47D8-840E-FB9FA5BC9AC0"}
{
  "uptime" : 1000000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,1",
  "coalitionID" : 99029,
  "osVersion" : {
    "train" : "macOS 15.5",
    "build" : "24F74",
    "releaseType" : "User"
  },
  "captureTime" : "2025-06-23 07:09:50.6946 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "69AE04A8-7040-47D8-840E-FB9FA5BC9AC0",
  "pid" : 21933,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-06-19 08:09:49.7817 -0500",
  "procStartAbsTime" : 23030749342318,
  "procExitAbsTime" : 26033689190360,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"ACF28FB2-42FE-58C2-8DE5-A9B04FE55DAD","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "5CD00815-A492-345C-021D-25B424AB78F6",
  "appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"],"state":"unavailable"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "bootSessionUUID" : "D0F15393-EBAE-4F26-B3FA-2E72EE20C036",
  "wakeTime" : 17,
  "sleepWakeUUID" : "330494AF-0F72-44D1-B6FE-1A2A615937FA",
  "sip" : "enabled",
  "vmRegionInfo" : "0xd9e091e3de8 is not in any region.  Bytes after previous region: 14491372633577  Bytes before following region: 90580707295768\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00000d9e091e3de8","rawCodes":[1,14972408970728],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000d9e091e3de8"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":21933},
  "vmregioninfo" : "0xd9e091e3de8 is not in any region.  Bytes after previous region: 14491372633577  Bytes before following region: 90580707295768\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "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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    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703356518400,
    "size" : 38264,
    "uuid" : "1fb5adb0-059e-3369-9c63-abde93e91499",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "arch" : "x86_64",
    "base" : 140703417610240,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 22356791,
    "uuid" : "c26f6f9e-8230-3c1f-8c48-02d9de58fbc8",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2575.60.5"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703452606464,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 5033928,
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    "name" : "SkyLight"
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    "size" : 291594,
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    "name" : "libdispatch.dylib"
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    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703355412480,
    "size" : 520192,
    "uuid" : "e9b27e7e-c40d-3405-a371-a753e116f54f",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
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],
  "sharedCache" : {
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},
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "14128c823c5f722cf860af03e8db617a8ce0b14c",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "64c17a9925d75a7281053d4c",
      "factorPackIds" : {
        "SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
      },
      "deploymentId" : 240000002
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    {
      "rolloutId" : "6410af69ed1e1e7ab93ed169",
      "factorPackIds" : {

      },
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    }
  ],
  "experiments" : [
    {
      "treatmentId" : "ccf01f2d-382e-4ccc-a332-b3f688bc9bbf",
      "experimentId" : "67f46b1a73932228c9baf274",
      "deploymentId" : 400000001
    }
  ]
},
  "reportNotes" : [
  "RIP register does not match crashing frame (0x0 vs 0x7FF89AE52AE0)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9blf

Summary of feedback from opening 9blf fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for ALA /A:2  
Atom H1 is not in the residue template for PHE /B:6  
Atom H1 is not in the residue template for SER /C:1  
Atom H1 is not in the residue template for PHE /D:6  
note | Fetching compressed mmCIF 9blf from http://files.rcsb.org/download/9blf.cif  
  
9blf title:  
SARS-CoV-2 core polymerase complex inhibited by araCTP [more info...]  
  
Chain information for 9blf #1  
---  
Chain | Description | UniProt  
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 2-929  
B D | Non-structural protein 8 | R1AB_SARS2 6-193  
C | Non-structural protein 7 | R1A_SARS2 1-73  
P | RNA (31-MER) |   
T | RNA (33-MER) |   
  
Non-standard residues in 9blf #1  
---  
CAR — cytosine arabinose-5'-phosphate  
HF4 —
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-
D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE)  
MG — magnesium ion  
ZN — zinc ion  
  

> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 UTP-UTP_rebuild_04_rnk.pdb"
> "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"
> "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 araUTP - UTP rebuild08_rnk.pdb"

Chain information for SARS2 UTP-UTP_rebuild_04_rnk.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
P | No description available  
T | No description available  
  
Chain information for SARS2_araUTP_15_rnk.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
P | No description available  
T | No description available  
  
Chain information for SARS2 araUTP - UTP rebuild08_rnk.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
P | No description available  
T | No description available  
  

> matchmaker #2-4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9blf, chain A (#1) with SARS2 UTP-UTP_rebuild_04_rnk.pdb, chain A
(#2), sequence alignment score = 4682.2  
RMSD between 927 pruned atom pairs is 0.364 angstroms; (across all 928 pairs:
0.379)  
  
Matchmaker 9blf, chain A (#1) with SARS2_araUTP_15_rnk.pdb, chain A (#3),
sequence alignment score = 4681  
RMSD between 925 pruned atom pairs is 0.373 angstroms; (across all 928 pairs:
0.393)  
  
Matchmaker 9blf, chain A (#1) with SARS2 araUTP - UTP rebuild08_rnk.pdb, chain
A (#4), sequence alignment score = 4671.4  
RMSD between 925 pruned atom pairs is 0.443 angstroms; (across all 928 pairs:
0.464)  
  

> show style stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style stick

Changed 60023 atom styles  

> delete H

> view ligand

> select ligand

87 atoms, 90 bonds, 3 residues, 2 models selected  

> select #1/A:1006@C2'

1 atom, 1 residue, 1 model selected  

> select up

29 atoms, 30 bonds, 1 residue, 1 model selected  

> view sel

> color byhetero

> set bgColor white

> hide #!4 models

> hide #!3 models

> hide #!2 models

> open 7uoe

7uoe title:  
SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic
state [more info...]  
  
Chain information for 7uoe #5  
---  
Chain | Description | UniProt  
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932  
B D | Non-structural protein 8 | R1AB_SARS2 1-198  
C | Non-structural protein 7 | R1AB_SARS2 1-83  
P | Product RNA (35-MER) |   
T | Template RNA (55-MER) |   
  
Non-standard residues in 7uoe #5  
---  
CTP — cytidine-5'-triphosphate  
L2B — 3'-deoxyuridine-5'-monophosphate
([(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-
oxolan-2-yl]methyl dihydrogen phosphate)  
MG — magnesium ion  
ZN — zinc ion  
  

> matchmaker #5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9blf, chain A (#1) with 7uoe, chain A (#5), sequence alignment
score = 4731.4  
RMSD between 917 pruned atom pairs is 0.957 angstroms; (across all 928 pairs:
1.004)  
  

> style stick

Changed 61344 atom styles  

> color byhetero

> open 6yyt

6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt #6  
---  
Chain | Description | UniProt  
A | nsp12 | R1AB_SARS2 1-932  
B D | nsp8 | R1AB_SARS2 1-198  
C | nsp7 | R1AB_SARS2 1-83  
P Q T U | RNA product |   
  
Non-standard residues in 6yyt #6  
---  
ZN — zinc ion  
  

> matchmaker #6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9blf, chain A (#1) with 6yyt, chain A (#6), sequence alignment
score = 4617.4  
RMSD between 840 pruned atom pairs is 0.695 angstroms; (across all 853 pairs:
0.848)  
  

> style stick

Changed 72719 atom styles  

> color byhetero

> hide #!5 models

> hide #!6 models

> show #!5 models

> show #!2 models

> hide #!5 models

> hide #!1 models

> hide #!2 models

> show #!4 models

> show #!5 models

> show #!3 models

> hide #!5 models

> hide #!4 models

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!5 models

> show #!6 models

> show #!5 models

> hide #!3 models

> hide #!5 models

> show #!2 models

> hide #!6 models

> show #!3 models

> hide #!3 models

> show #!6 models

> close #6

> show #!5 models

> hide #!5 models

> show #!1 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"

Chain information for SARS2_araUTP_15_rnk.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
P | No description available  
T | No description available  
  

> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 araUTP density map.mrc"

Opened SARS2 araUTP density map.mrc as #7, grid size 256,256,256, pixel 1.06,
shown at level 0.151, step 1, values float32  

> view #6

> volume #7 level 0.2634

> view ligand

> style stick

Changed 73464 atom styles  

> transparency 50

> select ligand

135 atoms, 140 bonds, 5 residues, 3 models selected  

> view #6

> volume #7 level 0.7138

> ui tool show "Side View"

> select #6/P:30@O3'

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> view sel

> close #6-7

> info #1

3 models  
#1, 9blf, hidden  
12293 atoms, 12678 bonds, 1444 residues, 6 chains (A,B,C,D,P,T)  
63 hydrogen bonds, 12 metal coordination bonds  
#1.1, hydrogen bonds, shown, 63 pseudobonds  
#1.2, metal coordination bonds, shown, 12 pseudobonds  

> open 9blf

Summary of feedback from opening 9blf fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for ALA /A:2  
Atom H1 is not in the residue template for PHE /B:6  
Atom H1 is not in the residue template for SER /C:1  
Atom H1 is not in the residue template for PHE /D:6  
  
9blf title:  
SARS-CoV-2 core polymerase complex inhibited by araCTP [more info...]  
  
Chain information for 9blf #6  
---  
Chain | Description | UniProt  
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 2-929  
B D | Non-structural protein 8 | R1AB_SARS2 6-193  
C | Non-structural protein 7 | R1A_SARS2 1-73  
P | RNA (31-MER) |   
T | RNA (33-MER) |   
  
Non-standard residues in 9blf #6  
---  
CAR — cytosine arabinose-5'-phosphate  
HF4 —
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-
D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE)  
MG — magnesium ion  
ZN — zinc ion  
  

> log metadata #6

Metadata for 9blf #6  
---  
Title | SARS-CoV-2 core polymerase complex inhibited by araCTP  
Citation | Anderson, T.K., Kirchdoerfer, R.N. (?). Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP. To Be Published  
Non-standard residues | CAR — cytosine arabinose-5'-phosphate  
HF4 —
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-
D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE)  
MG — magnesium ion  
ZN — zinc ion  
Gene sources | Severe acute respiratory syndrome coronavirus 2  
synthetic construct  
CryoEM Map | EMDB 44654 — open map  
Experimental method | Electron microscopy  
Resolution | 3.31Å  
  
> open 44654 fromDatabase emdb

Summary of feedback from opening 44654 fetched from emdb  
---  
notes | Fetching compressed map 44654 from https://files.wwpdb.org/pub/emdb/structures/EMD-44654/map/emd_44654.map.gz  
Fetching map header 44654 from
https://files.wwpdb.org/pub/emdb/structures/EMD-44654/header/emd-44654.xml  
  
Opened emdb 44654 as #7, grid size 256,256,256, pixel 1.06, shown at level
0.131, step 1, values float32, fit PDB 9blf  

> hide #!7 models

> style stick

Changed 85021 atom styles  

> delete H

> color byhetero

> select #6/P:31@C3'

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> view sel

> show #!7 models

> volume #7 level 0.3668

> transparency 50

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!5 models

> hide #!5 models

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

> open 7uoe

7uoe title:  
SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic
state [more info...]  
  
Chain information for 7uoe #8  
---  
Chain | Description | UniProt  
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932  
B D | Non-structural protein 8 | R1AB_SARS2 1-198  
C | Non-structural protein 7 | R1AB_SARS2 1-83  
P | Product RNA (35-MER) |   
T | Template RNA (55-MER) |   
  
Non-standard residues in 7uoe #8  
---  
CTP — cytidine-5'-triphosphate  
L2B — 3'-deoxyuridine-5'-monophosphate
([(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-
oxolan-2-yl]methyl dihydrogen phosphate)  
MG — magnesium ion  
ZN — zinc ion  
  

> matchmaker #8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9blf, chain A (#1) with 7uoe, chain A (#8), sequence alignment
score = 4731.4  
RMSD between 917 pruned atom pairs is 0.957 angstroms; (across all 928 pairs:
1.004)  
  

> style stick

Changed 86342 atom styles  

> color byhetero

> close #8

> open 6yyt

6yyt title:  
Structure of replicating SARS-CoV-2 polymerase [more info...]  
  
Chain information for 6yyt #8  
---  
Chain | Description | UniProt  
A | nsp12 | R1AB_SARS2 1-932  
B D | nsp8 | R1AB_SARS2 1-198  
C | nsp7 | R1AB_SARS2 1-83  
P Q T U | RNA product |   
  
Non-standard residues in 6yyt #8  
---  
ZN — zinc ion  
  

> matchmaker #8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9blf, chain A (#1) with 6yyt, chain A (#8), sequence alignment
score = 4617.4  
RMSD between 840 pruned atom pairs is 0.695 angstroms; (across all 853 pairs:
0.848)  
  

> style stick

Changed 85012 atom styles  

> color byhetero

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!6 models

> show #!3 models

> show #!5 models

> select #3/P:30@O3'

1 atom, 1 residue, 1 model selected  

> select add #8/P:18@O3'

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance #3/P:30@O3' #8/P:18@O3'

Distance between SARS2_araUTP_15_rnk.pdb #3/P UAT 30 O3' and 6yyt #8/P G 18
O3': 1.897Å  

> close #9

> hide #!7 models

> hide #!5 models

> hide #!3 models

> hide #!8 models

> show #!3 models

> show #!8 models

> hide #!3 models

> open 7uo9

7uo9 title:  
SARS-CoV-2 replication-transcription complex bound to UTP, in a pre-catalytic
state [more info...]  
  
Chain information for 7uo9 #9  
---  
Chain | Description | UniProt  
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932  
B D | Non-structural protein 8 | R1AB_SARS2 1-198  
C | Non-structural protein 7 | R1AB_SARS2 1-83  
P | Product RNA (35-MER) |   
T | Template RNA (55-MER) |   
  
Non-standard residues in 7uo9 #9  
---  
MG — magnesium ion  
UTP — uridine 5'-triphosphate  
ZN — zinc ion  
  

> matchmaker #9 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9blf, chain A (#1) with 7uo9, chain A (#9), sequence alignment
score = 4558.6  
RMSD between 912 pruned atom pairs is 0.929 angstroms; (across all 926 pairs:
1.004)  
  

> style stick

Changed 108875 atom styles  

> color byhetero

> delete H

> hide #!8 models

> hide #!9 models

> show #!1 models

> show #!7 models

> hide #!7 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 araUTP density map.mrc"

Opened SARS2 araUTP density map.mrc as #10, grid size 256,256,256, pixel 1.06,
shown at level 0.151, step 1, values float32  

> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"

Chain information for SARS2_araUTP_15_rnk.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
P | No description available  
T | No description available  
  

> hide #!3 models

> style stick

Changed 109690 atom styles  

> delete H

> transparency 50

> color byhetero

> volume #10 level 0.8489

> select :H8

Nothing selected  

> select H

Nothing selected  

> hide #!10 models

> hide #!11 models

> open 2lsc

Summary of feedback from opening 2lsc fetched from pdb  
---  
warnings | Atom HO5' is not in the residue template for CFL /A:1  
Atom HO5' is not in the residue template for CFL /B:13  
note | Fetching compressed mmCIF 2lsc from http://files.rcsb.org/download/2lsc.cif  
  
2lsc title:  
Solution structure of 2'F-ANA and ANA self-complementary duplex [more info...]  
  
Chain information for 2lsc  
---  
Chain | Description  
12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A 12.7/A 12.8/A 12.9/A 12.10/A 12.11/A 12.12/A 12.13/A 12.14/A 12.15/A 12.16/A 12.17/A 12.18/A 12.19/A 12.20/A 12.1/B 12.2/B 12.3/B 12.4/B 12.5/B 12.6/B 12.7/B 12.8/B 12.9/B 12.10/B 12.11/B 12.12/B 12.13/B 12.14/B 12.15/B 12.16/B 12.17/B 12.18/B 12.19/B 12.20/B | DNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')  
  

> view #12

> delete #12.2-20

> ~ribbon #12

> select #12.1/A:6@O2'

1 atom, 1 residue, 1 model selected  

> select add #12.1/A:6@C8

2 atoms, 1 residue, 1 model selected  

> ui tool show Distances

> distance #12.1/A:6@O2' #12.1/A:6@C8

Distance between 2lsc #12.1/A A5O 6 O2' and C8: 2.992Å  

> ~distance #12.1/A:6@O2' #12.1/A:6@C8

> select clear

> select #12.1/A:6@C8

1 atom, 1 residue, 1 model selected  

> select add #12.1/A:5@O2'

2 atoms, 2 residues, 1 model selected  

> distance #12.1/A:6@C8 #12.1/A:5@O2'

Distance between 2lsc #12.1/A A5O 6 C8 and A5O 5 O2': 3.285Å  

> addh H #12

Expected a keyword  

> addh #12

Summary of feedback from adding hydrogens to 2lsc #12.1  
---  
notes | Termini for 2lsc (#12.1) chain A determined from SEQRES records  
Termini for 2lsc (#12.1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
42 hydrogen bonds  
0 hydrogens added  
  

> ~distance #12.1/A:6@C8 #12.1/A:5@O2'

> select add #12.1/A:5@C8

3 atoms, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> select #12.1/A:5@O2'

1 atom, 1 residue, 1 model selected  

> select add #12.1/A:5@C8

2 atoms, 1 residue, 1 model selected  

> distance #12.1/A:5@O2' #12.1/A:5@C8

Distance between 2lsc #12.1/A A5O 5 O2' and C8: 3.253Å  

> ~distance #12.1/A:5@O2' #12.1/A:5@C8

> select #12.1/A:5@HO2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #12.1/A:5@HO2'

1 atom, 1 residue, 1 model selected  

> select add #12.1/A:5@C8

2 atoms, 1 residue, 1 model selected  

> distance #12.1/A:5@HO2' #12.1/A:5@C8

Distance between 2lsc #12.1/A A5O 5 HO2' and C8: 3.024Å  

> select #12.1/B:21@C6

1 atom, 1 residue, 1 model selected  

> select add #12.1/B:21@F

2 atoms, 1 residue, 1 model selected  

> distance #12.1/B:21@C6 #12.1/B:21@F

Distance between 2lsc #12.1/B CFL 21 C6 and F: 2.873Å  

> close #13

> hide #!12 models

> show #!3 models

> view #3

> select #3/P:30@C1'

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> view sel


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

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14Z00105LL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 25 days, 15 hours, 25 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        MZ279:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 4 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by pett, 4 months ago

Resolution: → duplicate
Status: assigned → closed
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