Opened 9 hours ago

Closed 100 minutes ago

#20338 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: halle.andrews-clark@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-26.3-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 0x000000031bb07000 (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 0x000000031ab04000 (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 0x0000000319b01000 (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 0x0000000318afe000 (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 0x0000000317afb000 (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 0x0000000316af8000 (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 0x0000000315af5000 (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 0x0000000314af2000 (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 0x0000000313aef000 (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 0x0000000312aec000 (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 0x0000000311ae9000 (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 0x0000000200d29e40 (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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._webp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.segment._segment (total: 64)


{"app_name":"ChimeraX","timestamp":"2026-05-15 19:33:50.00 +0200","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":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3 (25D125)","roots_installed":0,"name":"ChimeraX","incident_id":"BE7E9ABA-F65E-4DC9-B9E8-DAE89BB2C5D4"}
{
  "uptime" : 650000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "coalitionID" : 35484,
  "osVersion" : {
    "train" : "macOS 26.3",
    "build" : "25D125",
    "releaseType" : "User"
  },
  "captureTime" : "2026-05-15 17:00:31.6785 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "BE7E9ABA-F65E-4DC9-B9E8-DAE89BB2C5D4",
  "pid" : 38574,
  "translated" : true,
  "cpuType" : "X86-64",
  "procLaunch" : "2026-04-22 12:20:17.0198 +0200",
  "procStartAbsTime" : 6068180062453,
  "procExitAbsTime" : 15640806792737,
  "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":"33116714-09C9-5A00-BCA9-4034A28E2E8E","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "02E04C25-79CA-2EF6-F248-C1774882463F",
  "appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"],"state":"unavailable"},
  "developerMode" : 1,
  "bootProgressRegister" : "0x3f000000",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570490881,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "bootSessionUUID" : "3B7E11F8-EC7A-483F-8808-4B8A8C5E6BA1",
  "wakeTime" : 17308,
  "sleepWakeUUID" : "C87EB039-63F2-49BB-9AC9-842E3A0E6B26",
  "sip" : "disabled",
  "vmRegionInfo" : "0x309c000031ff is not in any region.  Bytes after previous region: 52965536707072  Bytes before following region: 52106543222273\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, 0x0000309c000031ff","rawCodes":[1,53446573044223],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000309c000031ff"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":38574},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x309c000031ff is not in any region.  Bytes after previous region: 52965536707072  Bytes before following region: 52106543222273\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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  "uuid" : "21e21a13-985d-34f6-bfe0-1fd3ff38209f"
},
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "c999421fae40fdddce8885e3f32bdb28ada583dc",
  "roots_installed" : 0,
  "bug_type" : "309",
  "trmStatus" : 1,
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : [

      ],
      "deploymentId" : 240000025
    },
    {
      "rolloutId" : "6434420a89ec2e0a7a38bf5a",
      "factorPackIds" : [

      ],
      "deploymentId" : 240000011
    }
  ],
  "experiments" : [

  ]
},
  "reportNotes" : [
  "RIP register does not match crashing frame (0x0 vs 0x7FF89C982B80)"
]
}
===== 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 "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2c.map"

Opened S2c.map as #1, grid size 400,400,400, pixel 1.32, shown at level 0.295,
step 2, values float32  

> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/s2a.map"

Opened s2a.map as #2, grid size 400,400,400, pixel 1.32, shown at level 0.281,
step 2, values float32  

> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2b.map"

Opened S2b.map as #3, grid size 400,400,400, pixel 1.32, shown at level 0.335,
step 2, values float32  

> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2c.map"

Opened S2c.map as #4, grid size 400,400,400, pixel 1.32, shown at level 0.295,
step 2, values float32  

> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2d.map"

Opened S2d.map as #5, grid size 400,400,400, pixel 1.32, shown at level 0.306,
step 2, values float32  

> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2e.map"

Opened S2e.map as #6, grid size 400,400,400, pixel 1.32, shown at level 0.226,
step 2, values float32  

> open "/Users/haandrew/Documents/progress/2026/Cryo-EM/2025-09-25/PDB
> 10.1038/S2f.map"

Opened S2f.map as #7, grid size 400,400,400, pixel 1.32, shown at level 0.188,
step 2, values float32  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 7 maps.  

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> open "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39
> and exit focus mask /NU/cryosparc_P1_J49_001_volume_map.mrc"
> "/Users/haandrew/Documents/progress/2025/Cryo-EM/100625 /3DV_tRNA/J39 and
> exit focus mask /NU/cryosparc_P1_J49_001_volume_map_sharp.mrc"

Opened cryosparc_P1_J49_001_volume_map.mrc as #8.1, grid size 128,128,128,
pixel 3.32, shown at level 1.03, step 1, values float32  
Opened cryosparc_P1_J49_001_volume_map_sharp.mrc as #8.2, grid size
128,128,128, pixel 3.32, shown at level 1.35, step 1, values float32  

> volume #8.1 level 0.2864

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> surface dust #8.1 size 33.2

> surface dust #8.2 size 33.2

> surface dust #1 size 13.2

> surface dust #2 size 13.2

> surface dust #3 size 13.2

> surface dust #4 size 13.2

> surface dust #5 size 13.2

> surface dust #6 size 13.2

> surface dust #7 size 13.2

> surface dust #8.1 size 33.2

> surface dust #8.2 size 33.2

> hide #!8.2 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> volume #4 level 0.08311

> volume #4 level 0.2105

> select add #8.1

2 models selected  

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #8.1,0.0025754,0.99857,-0.053465,5.7525,0.37284,0.048651,0.92662,-58.772,0.92789,-0.02232,-0.37218,83.452

> view matrix models
> #8.1,-0.18017,0.89814,-0.40111,136.33,0.98316,0.17715,-0.044956,-21.126,0.03068,-0.40245,-0.91493,465.95

> view matrix models
> #8.1,-0.063474,0.87885,-0.47286,130.14,0.9965,0.081644,0.017976,-15.856,0.054405,-0.47007,-0.88095,468.77

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #8.1,0.022353,0.89352,-0.44847,103.8,0.99913,-0.035808,-0.021544,17.061,-0.035309,-0.4476,-0.89354,485.49

> ui mousemode right "translate selected models"

> view matrix models
> #8.1,0.022353,0.89352,-0.44847,0.42301,0.99913,-0.035808,-0.021544,-147.26,-0.035309,-0.4476,-0.89354,355.36

> volume #4 level 0.3803

> ui mousemode right "rotate selected models"

> view matrix models
> #8.1,0.4097,0.6881,0.59889,-247.85,0.12708,0.60706,-0.78443,51.78,-0.90332,0.39749,0.16127,144.14

> volume #8.1 level 0.6263

> view matrix models
> #8.1,0.087383,-0.74178,-0.66492,398.42,-0.34416,0.6039,-0.71893,143.23,0.93484,0.29166,-0.20252,-164.28

> view matrix models
> #8.1,0.10202,-0.8194,-0.56407,391.47,-0.26506,0.52414,-0.80933,161.91,0.95882,0.23208,-0.16372,-164.47

> view matrix models
> #8.1,0.10386,-0.83529,-0.53991,389.58,-0.24676,0.50423,-0.82756,165.99,0.9635,0.21917,-0.15375,-164.72

> view matrix models
> #8.1,-0.65595,-0.56331,0.50241,283.05,-0.70482,0.69531,-0.14061,83.732,-0.27012,-0.44634,-0.85312,398.71

> view matrix models
> #8.1,0.086651,-0.88935,0.44893,201.49,0.27163,0.45464,0.84824,-283.14,-0.95849,0.048444,0.28097,208.45

> view matrix models
> #8.1,0.052105,-0.78867,0.6126,153.26,0.36271,0.58649,0.7242,-306.73,-0.93044,0.18446,0.31662,164.98

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,125.34,0.19061,0.6577,0.72876,-285.26,-0.97591,0.046711,0.2131,226.67

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,291.79,0.19061,0.6577,0.72876,-8.4476,-0.97591,0.046711,0.2131,362.25

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,244.74,0.19061,0.6577,0.72876,-219.96,-0.97591,0.046711,0.2131,632.84

> view matrix models
> #8.1,0.10611,-0.75183,0.65076,246.68,0.19061,0.6577,0.72876,-224.71,-0.97591,0.046711,0.2131,636.69

> ui mousemode right "rotate selected models"

> view matrix models
> #8.1,0.31806,-0.16268,0.93401,11.834,-0.49899,0.80895,0.31081,-19.283,-0.80613,-0.56492,0.17612,741.28

> view matrix models
> #8.1,0.53916,-0.49148,0.68393,86.78,0.023771,0.82062,0.57097,-191.12,-0.84187,-0.29159,0.45413,631.77

> view matrix models
> #8.1,-0.24334,-0.11057,-0.96362,515.65,0.69154,0.67685,-0.25229,-137.56,0.68012,-0.72777,-0.088242,502.77

> view matrix models
> #8.1,-0.70391,-0.095711,-0.70382,560.73,0.4136,0.75034,-0.51569,-37.957,0.57746,-0.65409,-0.48858,591.78

> view matrix models
> #8.1,-0.70355,-0.18675,-0.68567,576.93,0.35038,0.74827,-0.56331,-13.702,0.61826,-0.63657,-0.46101,573.21

> ui mousemode right "move picked models"

> view matrix models
> #8.1,-0.70355,-0.18675,-0.68567,704.12,0.35038,0.74827,-0.56331,83.401,0.61826,-0.63657,-0.46101,394.56

> view matrix models
> #8.1,-0.70355,-0.18675,-0.68567,616.62,0.35038,0.74827,-0.56331,147.29,0.61826,-0.63657,-0.46101,343.58

> fitmap #8.1 inMap #4

Fit map cryosparc_P1_J49_001_volume_map.mrc in map S2c.map using 55316 points  
correlation = 0.7929, correlation about mean = 0.38, overlap = 1.865e+04  
steps = 232, shift = 38.9, angle = 13.1 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to S2c.map
(#4) coordinates:  
Matrix rotation and translation  
-0.69218461 -0.23733703 -0.68158022 617.95909860  
0.17454387 0.86129906 -0.47717750 159.04125684  
0.70029630 -0.44926057 -0.55475223 339.84370085  
Axis 0.01935687 -0.95815714 0.28558748  
Axis point 232.28797415 0.00000000 331.17813189  
Rotation angle (degrees) 133.85366479  
Shift along axis -43.36965704  
  

> select subtract #8.1

Nothing selected  

> volume #8.2 level 1.313

> hide #!8.2 models

> volume #8.1 level 0.1794

> volume #4 level 0.09372

> volume #4 level 0.2052

> show #!3 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!2 models

> color #8.1 #424242ff models

> color #8.1 #919191ff models

> color #8.1 darkgrey models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.1966

> hide #!2 models

> show #!3 models

> volume #3 level 0.1677

> volume #3 level 0.2616

> color #1 #ff40ffff models

> fitmap #8.1 inMap #4

Fit map cryosparc_P1_J49_001_volume_map.mrc in map S2c.map using 134048 points  
correlation = 0.7325, correlation about mean = 0.5665, overlap = 2.127e+04  
steps = 40, shift = 0.0275, angle = 0.00667 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to S2c.map
(#4) coordinates:  
Matrix rotation and translation  
-0.69210611 -0.23735662 -0.68165311 617.97405655  
0.17459473 0.86128797 -0.47717891 159.00866787  
0.70036120 -0.44927148 -0.55466145 339.81498218  
Axis 0.01934824 -0.95815172 0.28560623  
Axis point 232.28987029 0.00000000 331.18544036  
Rotation angle (degrees) 133.84738051  
Shift along axis -43.34444050  
  

> fitmap #8.1 inMap #4

Fit map cryosparc_P1_J49_001_volume_map.mrc in map S2c.map using 134048 points  
correlation = 0.7325, correlation about mean = 0.5665, overlap = 2.127e+04  
steps = 40, shift = 0.0126, angle = 0.00329 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to S2c.map
(#4) coordinates:  
Matrix rotation and translation  
-0.69212505 -0.23738966 -0.68162238 617.98085236  
0.17458371 0.86126341 -0.47722726 159.03653587  
0.70034524 -0.44930110 -0.55465761 339.83111420  
Axis 0.01936174 -0.95814465 0.28562903  
Axis point 232.29298165 0.00000000 331.19715854  
Rotation angle (degrees) 133.84895580  
Shift along axis -43.34918724  
  

> mmaker #8.1 to #2

No 'to' model specified  

> mmaker #8.1, #2

> matchmaker #8.1, #2

Missing or invalid "matchAtoms" argument: only initial part "#8.1" of atom
specifier valid  

> mmaker #8.1 to #2

No 'to' model specified  

> mmaker #8.1 to map #2

> matchmaker #8.1 to map #2

Invalid "to" argument: invalid atoms specifier  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.779, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 124, shift = 0.75, angle = 0.674 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69929659 -0.23402528 -0.67543797 617.15957487  
0.16943802 0.86369735 -0.47467636 158.91165484  
0.69446025 -0.44638444 -0.56432783 343.08985010  
Axis 0.01980732 -0.95907260 0.28246667  
Axis point 232.39979995 0.00000000 330.30493069  
Rotation angle (degrees) 134.42407860  
Shift along axis -43.27208729  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 40, shift = 0.0204, angle = 0.00868 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69923656 -0.23393818 -0.67553029 617.14650158  
0.16948896 0.86375291 -0.47455705 158.84485588  
0.69450827 -0.44632257 -0.56431767 343.05774229  
Axis 0.01976540 -0.95908809 0.28241699  
Axis point 232.38882223 0.00000000 330.28574614  
Rotation angle (degrees) 134.41903424  
Shift along axis -43.26272695  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 44, shift = 0.0207, angle = 0.00795 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69929203 -0.23401936 -0.67544474 617.15837896  
0.16943791 0.86370364 -0.47466496 158.90828296  
0.69446487 -0.44637536 -0.56432932 343.08718388  
Axis 0.01980556 -0.95907441 0.28246064  
Axis point 232.39903032 0.00000000 330.30326961  
Rotation angle (degrees) 134.42370272  
Shift along axis -43.27307760  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 44, shift = 0.0254, angle = 0.00963 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69923164 -0.23392252 -0.67554080 617.14078691  
0.16948155 0.86377090 -0.47452697 158.83183567  
0.69451503 -0.44629597 -0.56433038 343.05286754  
Axis 0.01976282 -0.95909348 0.28239887  
Axis point 232.38665168 0.00000000 330.27906442  
Rotation angle (degrees) 134.41862558  
Shift along axis -43.26039591  
  

> fitmap #8.1 inMap #2

Fit map cryosparc_P1_J49_001_volume_map.mrc in map s2a.map using 134048 points  
correlation = 0.7791, correlation about mean = 0.6012, overlap = 2.036e+04  
steps = 40, shift = 0.0234, angle = 0.00333 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#8.1) relative to s2a.map
(#2) coordinates:  
Matrix rotation and translation  
-0.69925824 -0.23395586 -0.67550172 617.14809957  
0.16944160 0.86376114 -0.47455900 158.87165606  
0.69449799 -0.44629738 -0.56435024 343.06665000  
Axis 0.01978502 -0.95909118 0.28240513  
Axis point 232.39247403 0.00000000 330.28714869  
Rotation angle (degrees) 134.42088043  
Shift along axis -43.27833678  
  

[deleted to fit within ticket limits]


> fitmap #24 inMap #1

Fit molecule scRibosome-twoSND1_merge_for_P2J138.pdb (#24) to map
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) using 205688 atoms  
average map value = 0.88, steps = 60  
shifted from previous position = 9.67  
rotated from previous position = 0.0276 degrees  
atoms outside contour = 111402, contour level = 0.94121  
  
Position of scRibosome-twoSND1_merge_for_P2J138.pdb (#24) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99064266 0.13436821 -0.02392251 401.36483029  
0.13342491 0.99035186 0.03742938 -35.49783425  
0.02872103 0.03388728 -0.99901288 408.68500605  
Axis -0.06712206 -0.99758463 -0.01787539  
Axis point 199.17366828 0.00000000 207.31548317  
Rotation angle (degrees) 178.48804668  
Shift along axis 1.16625506  
  

> volume #1 level 0.461

> select subtract #1

Nothing selected  

> show #!23 models

> select add #24

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected  

> select subtract #24

Nothing selected  

> select add #23

205688 atoms, 220331 bonds, 17 pseudobonds, 17342 residues, 2 models selected  

> view matrix models #23,1,0,0,6.1177,0,1,0,145.1,0,0,1,-9.8481

> view matrix models #23,1,0,0,13.572,0,1,0,-78.83,0,0,1,-281.68

> view matrix models #23,1,0,0,296.63,0,1,0,-60.556,0,0,1,-116.11

> view matrix models #23,1,0,0,228.19,0,1,0,-419.6,0,0,1,-44.151

> view matrix models #23,1,0,0,-168.23,0,1,0,-245.53,0,0,1,-277.11

> view matrix models #23,1,0,0,-258.71,0,1,0,-365.84,0,0,1,-279.56

> ui mousemode right "rotate selected models"

> view matrix models
> #23,0.85379,0.19423,0.48303,-369.7,-0.49522,0.016707,0.86861,-247.84,0.16064,-0.98081,0.11045,73.342

> ui mousemode right "translate selected models"

> view matrix models
> #23,0.85379,0.19423,0.48303,-383.14,-0.49522,0.016707,0.86861,243.06,0.16064,-0.98081,0.11045,338.94

> view matrix models
> #23,0.85379,0.19423,0.48303,-193.15,-0.49522,0.016707,0.86861,152.79,0.16064,-0.98081,0.11045,370.48

> ui mousemode right "rotate selected models"

> view matrix models
> #23,0.68856,0.2938,0.663,-216.32,-0.45243,-0.54047,0.70937,289.7,0.56674,-0.7884,-0.23922,319.72

> ui mousemode right "translate selected models"

> view matrix models
> #23,0.68856,0.2938,0.663,-200.89,-0.45243,-0.54047,0.70937,241.45,0.56674,-0.7884,-0.23922,15.225

> fitmap #23 inMap #1

Fit molecule scRibosome-twoSND1_merge_for_P2J138.pdb (#23) to map
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) using 205688 atoms  
average map value = 0.88, steps = 140  
shifted from previous position = 30  
rotated from previous position = 25.2 degrees  
atoms outside contour = 41443, contour level = 0.461  
  
Position of scRibosome-twoSND1_merge_for_P2J138.pdb (#23) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99065654 0.13428559 -0.02381081 401.33628571  
0.13334686 0.99036335 0.03740292 -35.52823345  
0.02860401 0.03387835 -0.99901652 408.72103429  
Axis -0.06708154 -0.99758752 -0.01786641  
Axis point 199.17121351 0.00000000 207.32188921  
Rotation angle (degrees) 178.49462144  
Shift along axis 1.21789044  
  

> select subtract #23

Nothing selected  

> color zone #1 near #23

> hide #!24 models

> hide #!23 models

> color #1 #bfbebaff models

> show #!2 models

> select add #2

2 models selected  

> show #!3 models

> show #!4 models

> show #!5 models

> show #!7 models

> hide #!7 models

> hide #!4 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> volume #1 level 0.9958

> volume #2 level 0.9896

> volume #3 level 0.5326

> volume #4 level 0.6669

> volume #5 level 1.254

> volume #6 level 0.9946

> volume #7 level 1.297

> volume #8 level 1.036

> volume #9 level 1.595

> volume #10 level 1.044

> volume #11 level 1.112

> volume #14 level 0.6232

> volume #16 level 0.4208

> volume #17 level 0.9187

> volume #18 level 1.261

> volume #19 level 0.9165

> volume #19 level 0.878

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> select subtract #2

Nothing selected  

> hide #!25 models

> select add #2

2 models selected  

> view matrix models
> #2,0.60956,-0.76836,0.19511,501.52,-0.79273,-0.59228,0.14417,190.91,0.0047833,-0.24255,-0.97013,298.23

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.33071,0.52393,0.78494,158.34,-0.32262,-0.71886,0.61575,16.107,0.88687,-0.45688,-0.068703,-38.271

> view matrix models
> #2,0.21583,0.30389,0.92794,201.61,-0.24647,-0.9026,0.35293,94.313,0.94481,-0.30488,-0.11991,-73.397

> view matrix models
> #2,0.21588,0.304,0.92789,201.59,-0.24652,-0.90254,0.35305,94.282,0.94479,-0.30496,-0.1199,-73.379

> view matrix models
> #2,0.20489,0.2773,0.93868,207.56,-0.23594,-0.91676,0.32232,101.48,0.94992,-0.28752,-0.12241,-77.78

> view matrix models
> #2,0.24452,0.36822,0.89701,187.76,-0.27094,-0.86229,0.42783,75.257,0.93102,-0.34765,-0.11108,-62.899

> view matrix models
> #2,0.74017,0.22249,-0.63454,430.77,0.14714,-0.97439,-0.17002,132.62,-0.65612,0.032477,-0.75396,338.84

> view matrix models
> #2,0.76243,0.057781,-0.64448,463.79,-0.040989,-0.98969,-0.13722,170.56,-0.64577,0.13104,-0.7522,314.74

> view matrix models
> #2,0.73355,-0.20229,-0.64883,527.65,-0.33296,-0.93923,-0.083616,212.72,-0.59249,0.27737,-0.75632,272.02

> view matrix models
> #2,-0.15902,0.33589,-0.92838,665.83,-0.73531,-0.66778,-0.11566,249.06,-0.65881,0.66426,0.35317,-29.775

> view matrix models
> #2,-0.55938,0.59127,-0.58095,625.8,-0.11148,-0.74815,-0.6541,241.73,-0.82138,-0.30112,0.48441,188.66

> view matrix models
> #2,-0.5595,0.58136,-0.59075,630.04,-0.11041,-0.75867,-0.64205,241.26,-0.82144,-0.294,0.48866,186.23

> view matrix models
> #2,-0.55945,0.58506,-0.58712,628.46,-0.11081,-0.75478,-0.64655,241.44,-0.82142,-0.29666,0.4871,187.13

> view matrix models
> #2,-0.50031,0.6501,-0.57189,598.08,-0.23282,-0.73718,-0.63432,261.95,-0.83396,-0.18421,0.52017,158.5

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.50031,0.6501,-0.57189,380.81,-0.23282,-0.73718,-0.63432,528.29,-0.83396,-0.18421,0.52017,252.86

> view matrix models
> #2,-0.50031,0.6501,-0.57189,247.33,-0.23282,-0.73718,-0.63432,511.92,-0.83396,-0.18421,0.52017,23.275

> fitmap #2 inMap #1

Fit map cryosparc_P1_J49_001_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 23497 points  
correlation = 0.9913, correlation about mean = 0.8492, overlap = 5.084e+04  
steps = 120, shift = 20, angle = 18.2 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#2) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999995 -0.00020371 -0.00032536 0.14476519  
0.00020362 0.99999997 -0.00026248 0.03803555  
0.00032541 0.00026241 0.99999993 -0.14702941  
Axis 0.56438844 -0.69974138 0.43798137  
Axis point 439.42587188 0.00000000 460.99015298  
Rotation angle (degrees) 0.02664276  
Shift along axis -0.00930739  
  

> select subtract #2

Nothing selected  

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> select add #3

2 models selected  

> view matrix models
> #3,-0.81182,0.4742,-0.3407,454.52,-0.17891,0.35341,0.9182,-301.5,0.55582,0.80637,-0.20207,-63.972

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.19406,0.16832,0.96644,26.561,0.97847,0.037388,-0.20299,-237.31,-0.0703,0.98502,-0.15744,20.439

> view matrix models
> #3,-0.51197,-0.35704,0.78129,329.39,0.75379,0.24943,0.60794,-409.87,-0.41193,0.90017,0.14143,46.874

> view matrix models
> #3,-0.85847,0.48596,-0.16395,423.86,0.40617,0.83938,0.36122,-410.66,0.31315,0.2435,-0.91796,262.93

> view matrix models
> #3,0.036545,0.96106,0.27391,37.532,0.96105,0.041334,-0.27325,-219.37,-0.27393,0.27323,-0.92212,381.73

> view matrix models
> #3,-0.13839,0.72479,0.67492,39.416,0.91497,-0.16725,0.36722,-302.23,0.37905,0.66836,-0.64002,97.433

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.13839,0.72479,0.67492,-94.61,0.91497,-0.16725,0.36722,164.16,0.37905,0.66836,-0.64002,79.595

> view matrix models
> #3,-0.13839,0.72479,0.67492,-223.18,0.91497,-0.16725,0.36722,207.25,0.37905,0.66836,-0.64002,-52.851

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.25418,0.73602,0.62743,-190.87,0.83284,-0.16324,0.52889,189.03,0.4917,0.65699,-0.57149,-88.984

> view matrix models
> #3,0.24566,0.96936,-0.0012755,-211.99,0.4433,-0.11117,0.88945,182.76,0.86205,-0.21907,-0.45703,-2.7602

> ui mousemode right "move picked models"

> view matrix models
> #3,0.24566,0.96936,-0.0012755,-107.32,0.4433,-0.11117,0.88945,-91.296,0.86205,-0.21907,-0.45703,-144.39

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!4 models

> ui mousemode right "rotate selected models"

> select add #4

2 models selected  

> view matrix models
> #4,0.71459,-0.64679,-0.2665,260.74,0.30768,-0.051541,0.95009,-42.751,-0.62824,-0.76093,0.16218,483.61

> view matrix models
> #4,-0.47693,0.7383,-0.47693,262.65,-0.85078,-0.25153,0.46141,358.06,0.2207,0.62582,0.74809,-130.02

> view matrix models
> #4,-0.98658,-0.15677,-0.045656,475.37,0.10578,-0.40062,-0.91012,479.49,0.12439,-0.90273,0.41183,297.18

> view matrix models
> #4,-0.96149,0.26933,-0.054782,378.91,-0.1289,-0.61791,-0.77561,548.78,-0.24275,-0.73868,0.62883,294.16

> view matrix models
> #4,-0.98293,-0.13744,-0.12228,486.93,0.13091,-0.055573,-0.98984,415.97,0.12924,-0.98895,0.072617,388.29

> volume #4 level 0.445

> view matrix models
> #4,-0.95856,-0.19407,-0.20855,514.25,0.20861,0.02038,-0.97779,380.3,0.19401,-0.98078,0.020949,384.94

> view matrix models
> #4,0.82621,0.21936,0.5189,-117.48,-0.12815,-0.82376,0.55227,281.39,0.54859,-0.52279,-0.65249,366.44

> view matrix models
> #4,0.20859,0.56612,-0.79749,240.27,0.94577,-0.32438,0.017104,71.625,-0.24901,-0.75781,-0.60309,573.04

> view matrix models
> #4,-0.97879,-0.020749,-0.20382,479.36,0.19302,-0.42688,-0.88347,459.82,-0.068677,-0.90407,0.42183,330.1

> view matrix models
> #4,-0.97741,-0.14598,-0.15287,494.74,0.17364,-0.14212,-0.9745,422.49,0.12054,-0.97902,0.16426,366.7

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.97741,-0.14598,-0.15287,378.24,0.17364,-0.14212,-0.9745,451.95,0.12054,-0.97902,0.16426,99.337

> view matrix models
> #4,-0.97741,-0.14598,-0.15287,410.06,0.17364,-0.14212,-0.9745,361.63,0.12054,-0.97902,0.16426,54.573

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!5 models

> select add #5

2 models selected  

> view matrix models
> #5,0.94884,0.21626,0.23005,-269.88,-0.16928,0.96347,-0.20754,279.73,-0.26653,0.15798,0.95079,-90.569

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.44586,-0.32097,0.83557,3.6126,-0.64601,0.76155,-0.052174,387.95,-0.61958,-0.56305,-0.5469,450.12

> view matrix models
> #5,-0.76512,-0.086479,0.63806,63.943,0.48487,0.57464,0.65931,39.004,-0.42367,0.81383,-0.39773,93.615

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.76512,-0.086479,0.63806,200.21,0.48487,0.57464,0.65931,-205.78,-0.42367,0.81383,-0.39773,-92.572

> fitmap #2 inMap #1

Fit map cryosparc_P1_J49_001_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 23497 points  
correlation = 0.9911, correlation about mean = 0.8469, overlap = 5.107e+04  
steps = 36, shift = 0.0443, angle = 0.0237 degrees  
  
Position of cryosparc_P1_J49_001_volume_map.mrc (#2) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00021951 -0.00008997 0.06408117  
0.00021951 0.99999999 0.00007828 -0.06929975  
0.00008995 -0.00007830 1.00000001 -0.02395475  
Axis -0.31338734 -0.36009777 0.87870244  
Axis point 342.26518886 268.79245294 0.00000000  
Rotation angle (degrees) 0.01431322  
Shift along axis -0.01617664  
  

> fitmap #3 inMap #1

Fit map cryosparc_P1_J97_002_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 56198 points  
correlation = 0.5786, correlation about mean = 0.03341, overlap = 1.661e+04  
steps = 152, shift = 18.5, angle = 15.1 degrees  
  
Position of cryosparc_P1_J97_002_volume_map_sharp.mrc (#3) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.87979777 -0.34466184 0.32735926 407.44281122  
-0.43817443 0.85500994 -0.27741875 183.79832786  
-0.18427977 -0.38751286 -0.90325785 534.81482134  
Axis -0.20708441 0.96238090 -0.17589498  
Axis point 261.08369443 0.00000000 255.57628817  
Rotation angle (degrees) 164.58435252  
Shift along axis -1.56229845  
  

> fitmap #4 inMap #1

Fit map cryosparc_P1_J97_002_volume_map.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 78366 points  
correlation = 0.5652, correlation about mean = 0.06789, overlap = 2.024e+04  
steps = 144, shift = 26.6, angle = 14.2 degrees  
  
Position of cryosparc_P1_J97_002_volume_map.mrc (#4) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46898217 0.88131733 0.05775364 -73.54777001  
-0.79252681 0.39106890 0.46793842 203.57879115  
0.38981659 -0.26522608 0.88187195 7.18313422  
Axis -0.39474823 -0.17878834 -0.90122614  
Axis point 126.36767626 165.79033932 0.00000000  
Rotation angle (degrees) 68.22507164  
Shift along axis -13.83828953  
  

> fitmap #5 inMap #1

Fit map cryosparc_P1_J98_001_volume_map_sharp.mrc in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 15013 points  
correlation = 0.6197, correlation about mean = 0.04936, overlap = 1.153e+04  
steps = 88, shift = 13.6, angle = 10.1 degrees  
  
Position of cryosparc_P1_J98_001_volume_map_sharp.mrc (#5) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.81731865 -0.54494787 0.18714172 121.60855897  
-0.55683584 -0.83051286 0.01349835 504.24650714  
0.14806770 -0.11523967 -0.98224017 411.79027378  
Axis -0.95318149 0.28930554 -0.08801903  
Axis point 0.00000000 277.87043769 191.30673445  
Rotation angle (degrees) 176.12782894  
Shift along axis -6.27909781  
  

> volume #5 level 1.188

> hide #!5 models

> select subtract #5

Nothing selected  

> show #!6 models

> ui mousemode right "rotate selected models"

> select add #6

2 models selected  

> view matrix models
> #6,0.90257,-0.41067,-0.12934,132.18,0.07275,0.44154,-0.89429,289.66,0.42436,0.79774,0.42839,-130.87

> view matrix models
> #6,-0.85783,-0.44324,0.26011,421.16,-0.27693,0.82503,0.49258,-11.114,-0.43293,0.35052,-0.83048,406.06

> view matrix models
> #6,-0.86753,-0.053706,0.49448,293.25,0.30129,0.73426,0.60834,-136.86,-0.39575,0.67674,-0.62082,286.71

> view matrix models
> #6,-0.95166,-0.041373,0.30437,348.5,0.2678,0.37355,0.88811,-115.05,-0.15044,0.92669,-0.34441,125.75

> volume #6 level 0.7556

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.95166,-0.041373,0.30437,456.4,0.2678,0.37355,0.88811,-189.89,-0.15044,0.92669,-0.34441,-70.403

> view matrix models
> #6,-0.95166,-0.041373,0.30437,317.78,0.2678,0.37355,0.88811,-156.3,-0.15044,0.92669,-0.34441,-187.06

> hide #!6 models

> show #!21 models

> show #!20 models

> show #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> select add #14

4 models selected  

> select add #15

6 models selected  

> select add #16

8 models selected  

> select add #17

10 models selected  

> select add #18

12 models selected  

> select add #19

14 models selected  

> select add #20

16 models selected  

> select add #21

18 models selected  

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!14 models

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.88863,-0.35545,0.28981,466.04,-0.068651,0.72789,0.68225,-248.5,-0.45346,0.58637,-0.67123,78.622,#14,-0.79261,0.43289,0.4294,172.45,0.39433,0.90107,-0.18051,-43.826,-0.46506,0.026247,-0.88489,481.71,#15,-0.79258,0.43287,0.42947,172.43,0.39437,0.90107,-0.18041,-43.883,-0.46508,0.026384,-0.88488,481.71,#16,-0.7966,0.37665,0.47283,178.01,0.30847,0.92594,-0.21789,-22.874,-0.51988,-0.027716,-0.85379,496.84,#17,-0.79683,0.37661,0.47247,178.13,0.30835,0.92595,-0.21805,-22.841,-0.5196,-0.028065,-0.85395,496.9,#18,-0.74248,0.48064,0.46659,145.92,0.40785,0.87692,-0.25432,-25.385,-0.53139,0.0014652,-0.84712,493.46,#19,-0.74263,0.48026,0.46675,146,0.4075,0.87713,-0.25415,-25.399,-0.53146,0.0014656,-0.84708,493.45,#20,0.059324,-0.97133,0.23022,341.19,0.80043,0.1841,0.57045,-134.36,-0.59648,0.15044,0.7884,119.57,#21,0.059493,-0.97129,0.23035,341.13,0.80047,0.18429,0.57034,-134.43,-0.59642,0.15045,0.78845,119.55

> view matrix models
> #6,-0.27537,0.061818,-0.95935,327.62,-0.81741,0.51018,0.2675,42.66,0.50597,0.85785,-0.089956,-297.6,#14,-0.56346,-0.53499,-0.62952,547.48,-0.48092,0.83199,-0.27661,182.35,0.67174,0.14689,-0.72608,174.33,#15,-0.5635,-0.53488,-0.62958,547.51,-0.48088,0.83205,-0.27649,182.3,0.67173,0.14695,-0.72608,174.31,#16,-0.55667,-0.59002,-0.58481,546.97,-0.56265,0.7857,-0.25712,206.01,0.61119,0.18591,-0.76934,186.11,#17,-0.55636,-0.5903,-0.58482,546.99,-0.56273,0.7855,-0.25752,206.13,0.61139,0.18582,-0.7692,186.05,#18,-0.62762,-0.54332,-0.55758,547.51,-0.47399,0.83484,-0.27996,182.84,0.6176,0.088575,-0.78149,208.7,#19,-0.62746,-0.54342,-0.55766,547.5,-0.47432,0.83473,-0.27973,182.88,0.61751,0.088988,-0.78151,208.63,#20,-0.95623,0.066098,0.28506,300.07,0.23274,-0.41866,0.87781,54.633,0.17737,0.90573,0.38495,-126.17,#21,-0.95621,0.065993,0.28516,300.1,0.2329,-0.41851,0.87784,54.543,0.17727,0.90581,0.38481,-126.16

> view matrix models
> #6,0.6015,0.44356,-0.66442,-50.318,-0.62157,0.78231,-0.040438,-83.433,0.50185,0.43731,0.74627,-202.41,#14,0.43201,-0.52635,-0.73234,348.95,-0.33465,0.6605,-0.67213,268.59,0.83748,0.53544,0.1092,-117.32,#15,0.43197,-0.52628,-0.73242,348.97,-0.33463,0.6606,-0.67203,268.54,0.83751,0.53539,0.10925,-117.36,#16,0.42653,-0.50425,-0.75087,346.98,-0.42797,0.61884,-0.65869,293.9,0.79682,0.6023,0.048154,-109.99,#17,0.42688,-0.50437,-0.75059,346.9,-0.42789,0.61857,-0.659,294,0.79667,0.60248,0.04824,-110.04,#18,0.3566,-0.57519,-0.7362,374.34,-0.36451,0.63989,-0.67651,281.42,0.86021,0.5096,0.018522,-98.028,#19,0.35676,-0.57489,-0.73636,374.27,-0.3648,0.63992,-0.67633,281.42,0.86003,0.50991,0.018579,-98.062,#20,-0.4484,0.89294,0.039979,58.278,0.025513,-0.031923,0.99916,-18.06,0.89347,0.44905,-0.0084671,-83.148,#21,-0.44853,0.89288,0.039909,58.335,0.025626,-0.031787,0.99917,-18.131,0.8934,0.44918,-0.0086234,-83.169

> volume #15 level 0.723

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.6015,0.44356,-0.66442,40.545,-0.62157,0.78231,-0.040438,-173.99,0.50185,0.43731,0.74627,-400.35,#14,0.43201,-0.52635,-0.73234,439.81,-0.33465,0.6605,-0.67213,178.03,0.83748,0.53544,0.1092,-315.26,#15,0.43197,-0.52628,-0.73242,439.83,-0.33463,0.6606,-0.67203,177.98,0.83751,0.53539,0.10925,-315.29,#16,0.42653,-0.50425,-0.75087,437.84,-0.42797,0.61884,-0.65869,203.34,0.79682,0.6023,0.048154,-307.92,#17,0.42688,-0.50437,-0.75059,437.76,-0.42789,0.61857,-0.659,203.44,0.79667,0.60248,0.04824,-307.97,#18,0.3566,-0.57519,-0.7362,465.2,-0.36451,0.63989,-0.67651,190.86,0.86021,0.5096,0.018522,-295.96,#19,0.35676,-0.57489,-0.73636,465.13,-0.3648,0.63992,-0.67633,190.86,0.86003,0.50991,0.018579,-296,#20,-0.4484,0.89294,0.039979,149.14,0.025513,-0.031923,0.99916,-108.62,0.89347,0.44905,-0.0084671,-281.08,#21,-0.44853,0.89288,0.039909,149.2,0.025626,-0.031787,0.99917,-108.69,0.8934,0.44918,-0.0086234,-281.1

> view matrix models
> #6,0.6015,0.44356,-0.66442,-42.139,-0.62157,0.78231,-0.040438,-120.02,0.50185,0.43731,0.74627,-488.42,#14,0.43201,-0.52635,-0.73234,357.13,-0.33465,0.6605,-0.67213,232,0.83748,0.53544,0.1092,-403.33,#15,0.43197,-0.52628,-0.73242,357.15,-0.33463,0.6606,-0.67203,231.96,0.83751,0.53539,0.10925,-403.36,#16,0.42653,-0.50425,-0.75087,355.16,-0.42797,0.61884,-0.65869,257.32,0.79682,0.6023,0.048154,-395.99,#17,0.42688,-0.50437,-0.75059,355.07,-0.42789,0.61857,-0.659,257.41,0.79667,0.60248,0.04824,-396.04,#18,0.3566,-0.57519,-0.7362,382.52,-0.36451,0.63989,-0.67651,244.83,0.86021,0.5096,0.018522,-384.03,#19,0.35676,-0.57489,-0.73636,382.45,-0.3648,0.63992,-0.67633,244.83,0.86003,0.50991,0.018579,-384.06,#20,-0.4484,0.89294,0.039979,66.457,0.025513,-0.031923,0.99916,-54.646,0.89347,0.44905,-0.0084671,-369.15,#21,-0.44853,0.89288,0.039909,66.514,0.025626,-0.031787,0.99917,-54.717,0.8934,0.44918,-0.0086234,-369.17

> fitmap #21 inMap #1

Fit map cryosparc_P1_J108_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 50668 points  
correlation = 0.9363, correlation about mean = 0.5931, overlap = 4.442e+04  
steps = 116, shift = 10.6, angle = 15.6 degrees  
  
Position of cryosparc_P1_J108_001_volume_map.mrc z flip (#21) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69722091 -0.66681163 0.26314484 446.15123279  
-0.64056974 0.41474667 -0.64626276 393.21069291  
0.32179709 -0.61915055 -0.71630942 437.70886650  
Axis 0.38875619 -0.84100200 0.37627683  
Axis point 309.44766119 0.00000000 311.41465143  
Rotation angle (degrees) 178.00166477  
Shift along axis 7.45278003  
  

> fitmap #20 inMap #1

Fit map cryosparc_P1_J108_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 20960 points  
correlation = 0.9607, correlation about mean = 0.5066, overlap = 3.58e+04  
steps = 100, shift = 8.98, angle = 15.6 degrees  
  
Position of cryosparc_P1_J108_001_volume_map_sharp.mrc z flip (#20) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.69735507 -0.66659148 0.26334711 446.11538956  
-0.64075788 0.41520272 -0.64578327 393.12728635  
0.32113119 -0.61908197 -0.71666746 437.90594299  
Axis 0.38867981 -0.84113914 0.37604914  
Axis point 309.44378721 0.00000000 311.35730259  
Rotation angle (degrees) 178.03157705  
Shift along axis 7.39545109  
  

> fitmap #19 inMap #1

Fit map cryosparc_P1_J104_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 31946 points  
correlation = 0.9726, correlation about mean = 0.6536, overlap = 4.68e+04  
steps = 112, shift = 13.1, angle = 15.6 degrees  
  
Position of cryosparc_P1_J104_001_volume_map.mrc z flip (#19) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98937200 -0.14536553 0.00344927 453.78968015  
0.14529255 -0.98925754 -0.01611153 396.24423525  
0.00575427 -0.01543915 0.99986424 2.15653353  
Axis 0.00231325 -0.00793004 0.99996588  
Axis point 212.41805692 214.70699134 0.00000000  
Rotation angle (degrees) 171.64337919  
Shift along axis 0.06395459  
  

> fitmap #18 inMap #1

Fit map cryosparc_P1_J104_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 25838 points  
correlation = 0.9686, correlation about mean = 0.5898, overlap = 5.954e+04  
steps = 100, shift = 12.7, angle = 15.6 degrees  
  
Position of cryosparc_P1_J104_001_volume_map_sharp.mrc z flip (#18) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98947804 -0.14464737 0.00321708 453.69601027  
0.14458044 -0.98936883 -0.01567800 396.25026367  
0.00545066 -0.01504791 0.99987191 2.14304979  
Axis 0.00217846 -0.00772232 0.99996781  
Axis point 212.44320093 214.62382300 0.00000000  
Rotation angle (degrees) 171.68480854  
Shift along axis 0.07136871  
  

> fitmap #17 inMap #1

Fit map cryosparc_P1_J103_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 29219 points  
correlation = 0.9806, correlation about mean = 0.6608, overlap = 4.488e+04  
steps = 112, shift = 13.1, angle = 15.6 degrees  
  
Position of cryosparc_P1_J103_001_volume_map.mrc z flip (#17) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96680237 -0.25502082 -0.01604854 475.63744719  
0.25550434 -0.96561874 -0.04793720 375.10677453  
-0.00327179 -0.05044627 0.99872141 13.30973048  
Axis -0.00491309 -0.02501855 0.99967491  
Axis point 213.49188633 218.60521419 0.00000000  
Rotation angle (degrees) 165.20593606  
Shift along axis 1.58392768  
  

> fitmap #16 inMap #1

Fit map cryosparc_P1_J103_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 83702 points  
correlation = 0.9443, correlation about mean = 0.7798, overlap = 8.775e+04  
steps = 112, shift = 15.1, angle = 15.6 degrees  
  
Position of cryosparc_P1_J103_001_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96685076 -0.25484220 -0.01597028 475.59698170  
0.25532241 -0.96566039 -0.04806728 375.14545317  
-0.00317229 -0.05055146 0.99871641 13.35686200  
Axis -0.00486777 -0.02507780 0.99967365  
Axis point 213.48660701 218.60044325 0.00000000  
Rotation angle (degrees) 165.21660343  
Shift along axis 1.62958078  
  

> fitmap #15 inMap #1

Fit map cryosparc_P1_J98_001_volume_map.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 37686 points  
correlation = 0.941, correlation about mean = 0.482, overlap = 4.055e+04  
steps = 92, shift = 13.8, angle = 15.6 degrees  
  
Position of cryosparc_P1_J98_001_volume_map.mrc z flip (#15) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98115626 -0.17548487 -0.08085450 474.87934814  
0.17989885 -0.98236532 -0.05093882 396.45924831  
-0.07048966 -0.06452457 0.99542341 29.22298152  
Axis -0.03818429 -0.02913154 0.99884599  
Axis point 220.20435859 219.96923969 0.00000000  
Rotation angle (degrees) 169.75270090  
Shift along axis -0.49313815  
  

> fitmap #14 inMap #1

Fit map cryosparc_P1_J98_001_volume_map_sharp.mrc z flip in map
cryosparc_P1_J49_001_volume_map_sharp.mrc using 57626 points  
correlation = 0.9156, correlation about mean = 0.5549, overlap = 5.979e+04  
steps = 108, shift = 14.7, angle = 15.6 degrees  
  
Position of cryosparc_P1_J98_001_volume_map_sharp.mrc z flip (#14) relative to
cryosparc_P1_J49_001_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98115541 -0.17563607 -0.08053577 474.88496525  
0.18003760 -0.98233398 -0.05105281 396.45902867  
-0.07014630 -0.06459020 0.99544341 29.15850208  
Axis -0.03801754 -0.02917709 0.99885102  
Axis point 220.18894103 219.98655737 0.00000000  
Rotation angle (degrees) 169.74430222  
Shift along axis -0.49648181  
  

> select subtract #21

16 models selected  

> select subtract #20

14 models selected  

> select subtract #19

12 models selected  

> select subtract #18

10 models selected  

> select subtract #17

8 models selected  

> select subtract #16

6 models selected  

> select subtract #15

4 models selected  

> select subtract #14

2 models selected  

> show #!16 models

> hide #!16 models

> volume #1 level 0.1227

> hide #!1 models

> volume #1 level 0.4283

> volresample #14 ongrid #1

Unknown command: volresample #14 ongrid #1  

> volume resample #14 onGrid #1

Opened cryosparc_P1_J98_001_volume_map_sharp.mrc z flip resampled as #26, grid
size 128,128,128, pixel 3.32, shown at step 1, values float32  

> volume resample #3 onGrid #1

Opened cryosparc_P1_J97_002_volume_map_sharp.mrc resampled as #27, grid size
128,128,128, pixel 3.32, shown at step 1, values float32  

> hide #!27 models

> volume resample #16 onGrid #1

Opened cryosparc_P1_J103_001_volume_map_sharp.mrc z flip resampled as #28,
grid size 128,128,128, pixel 3.32, shown at step 1, values float32  

> show #!20 models

> volume #20 level 0.5538

> surface dust #1 size 33.2

> surface dust #15 size 33.2

> surface dust #20 size 33.2

> surface dust #26 size 33.2

> surface dust #28 size 33.2

> volume resample #20 onGrid #1

Opened cryosparc_P1_J108_001_volume_map_sharp.mrc z flip resampled as #29,
grid size 128,128,128, pixel 3.32, shown at step 1, values float32  

> volume morph #26-30

Opened morph as #30, grid size 128,128,128, pixel 3.32, shown at step 1,
values float32  

> select subtract #6

Nothing selected  

> hide #!30 models

> hide #!15 models

> volume #1 level 0.2209

> volume #1 level 0.3082

> hide #!1 models

> show #!26 models

> volume #26 level 0.1946

> volume #26 level 0.2335

> volume #27 level 0.4201

> hide #!27 models

> volume #28 level 0.1795

> show #!29 models

> hide #!28 models

> hide #!26 models

> volume #29 level 0.4606

> surface dust #29 size 33.2

> volume #29 level 0.4199

> show #!18 models

> volume resample #18 onGrid #1

Opened cryosparc_P1_J104_001_volume_map_sharp.mrc z flip resampled as #31,
grid size 128,128,128, pixel 3.32, shown at step 1, values float32  

> volume #31 level 0.4527

> volume morph #1,26,28,29,31

Opened morph as #32, grid size 128,128,128, pixel 3.32, shown at step 1,
values float32  

> surface dust #32 size 33.2

> show #!1 models

> hide #!1 models

> color #32 #d0dcd0ff models

> color #32 #dadccaff models

> color #32 #8d8e82ff models

> color #32 #8d8f83ff models

> color #32 #919191ff models

> color #32 #797979ff models

> volume #32 level 0.2864

> volume #32 color #e9e9c7

> volume #32 color #fbb5fb

> volume #32 style image

> volume #32 style surface

> volume #32 style mesh

> volume #32 style image maximumIntensityProjection true

> volume #32 region 0,0,63,127,127,63 step 1 maximumIntensityProjection false
> showOutlineBox true

> volume #32 region 0,0,0,127,127,127 step 1

> volume #32 region 0,0,0,127,127,127 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 63,63,63 imageMode orthoplanes

> volume #32 imageMode "box faces"

> volume #32 style surface

> volume #32

> volume #32 style image

> volume #32 style surface

> volume #!32 showOutlineBox false


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

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

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




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
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: MacBookPro17,1
      Model Number: Z11D000L9D/A
      Chip: Unknown
      Total Number of Cores: 8 (4 Performance and 4 Efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3 (25D125)
      Kernel Version: Darwin 25.3.0
      Time since boot: 45 days, 18 hours, 47 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2722H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          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-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 101 minutes ago

Cc: Eric Pettersen added
Component: Unassigned → Window Toolkit
Description: modified (diff)
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 Eric Pettersen, 100 minutes ago

Resolution: → duplicate
Status: assigned → closed

Hi Halle,

Thanks for reporting this problem. I would recommend upgrading to the latest ChimeraX release, which uses a newer version of the QT windowing toolkit with many bug fixes.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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