id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18815	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-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 0x0000000315a67000 (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 0x0000000314a5b000 (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 0x0000000313a4f000 (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 0x0000000312a43000 (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 0x0000000311a37000 (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 0x0000000310a2b000 (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 0x000000030fa1f000 (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 0x000000030ea13000 (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 0x000000030da07000 (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 0x000000030c9fb000 (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 0x000000030b9ef000 (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 0x00000002009020c0 (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.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics (total: 49)


{""app_name"":""ChimeraX"",""timestamp"":""2025-09-18 14:48:32.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.6.1 (24G90)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""CD466744-8B4B-4D28-B5B8-79B222F3F8C7""}
{
  ""uptime"" : 320000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 502,
  ""deployVersion"" : 210,
  ""modelCode"" : ""Mac14,7"",
  ""coalitionID"" : 38690,
  ""osVersion"" : {
    ""train"" : ""macOS 15.6.1"",
    ""build"" : ""24G90"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2025-09-18 14:48:23.2295 +0200"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""CD466744-8B4B-4D28-B5B8-79B222F3F8C7"",
  ""pid"" : 93187,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2025-09-18 10:53:43.8096 +0200"",
  ""procStartAbsTime"" : 7604542938598,
  ""procExitAbsTime"" : 7792712072039,
  ""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"":""C8D5DC0B-60ED-55CE-BACE-10C1ABEF1693"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""A032151A-3102-DB1C-CE1A-78095CA33466"",
  ""appleIntelligenceStatus"" : {""state"":""available""},
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""codeSigningAuxiliaryInfo"" : 0,
  ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""},
  ""bootSessionUUID"" : ""F60DD3ED-E170-4295-B791-EB2844EFB877"",
  ""wakeTime"" : 933,
  ""sleepWakeUUID"" : ""997E40FC-801A-4A69-8C7F-BB52CF833485"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0xad400068c3b is not in any region.  Bytes after previous region: 11424613436476  Bytes before following region: 93647466492869\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, 0x00068ad400068c3b"",""rawCodes"":[1,1841492998392891],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00068ad400068c3b -> 0x00000ad400068c3b (possible pointer authentication failure)""},
  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":93187},
  ""vmregioninfo"" : ""0xad400068c3b is not in any region.  Bytes after previous region: 11424613436476  Bytes before following region: 93647466492869\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  "",
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  ""faultingThread"" : 0,
  ""threads"" : 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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=4.1G written=226.9M(5%) resident=2570K(0%) swapped_out=224.4M(5%) unallocated=3.9G(95%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                           848K       30 \nColorSync                          624K       33 \nCoreAnimation                     2416K      139 \nCoreGraphics                        48K        3 \nCoreUI image data                 3344K       44 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             3.2G      176 \nMALLOC guard page                  288K       18 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        768K       48 \nStack                            331.2M       49 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      485.8M      311 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__AUTH                            5521K      697 \n__AUTH_CONST                      77.4M      944 \n__CTF                               824        1 \n__DATA                            33.9M     1078 \n__DATA_CONST                      36.7M     1096 \n__DATA_DIRTY                      2777K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       646.0M      146 \n__OBJC_RO                         61.4M        1 \n__OBJC_RW                         2396K        1 \n__TEXT                             1.1G     1022 \n__TEXT (graphics)                214.7M       94 \n__TPRO_CONST                       128K        2 \ndyld private memory                640K        6 \nmapped file                      313.3M       83 \npage table in kernel              2570K        1 \nshared memory                     3936K       29 \n===========                     =======  ======= \nTOTAL                              6.6G     6412 \nTOTAL, minus reserved VM space     6.5G     6412 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""150bb2f3b9f1f0ec5be4e127f3853e36e814d4f5"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""6297d96be2c9387df974efa4"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000032
    },
    {
      ""rolloutId"" : ""642da32dea3b2418c750f848"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000011
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"",
      ""experimentId"" : ""6685b283afc7c17197d69eec"",
      ""deploymentId"" : 400000012
    }
  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_rings/motl_M7_rf58_1_rings_per13n30_bin4_1.em
> format motl

Summary of feedback from opening
/Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_rings/motl_M7_rf58_1_rings_per13n30_bin4_1.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list motl_M7_rf58_1_rings_per13n30_bin4_1.em with 308
particles.  

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_centers/motl_M7_rf58_1_centers_per13n30_bin4_1_gamma_min_orientation_1.em
> format motl

Summary of feedback from opening
/Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_centers/motl_M7_rf58_1_centers_per13n30_bin4_1_gamma_min_orientation_1.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list
motl_M7_rf58_1_centers_per13n30_bin4_1_gamma_min_orientation_1.em with 53
particles.  

> artiax hide axes

> hide #!1.2.2 models

> hide #!1.2.1 models

> show #!1.2.1 models

> show #!1.2.2 models

> hide #!1.2.1 models

> show #!1.2.1 models

> open /Users/eunyoung/Downloads/M7_rf54_bin8_30_symmetrized.em

Opened M7_rf54_bin8_30_symmetrized.em as #2, grid size 104,104,104, pixel 1,
shown at level 0.107, step 1, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened M7_rf54_bin8_30_symmetrized.em as #1.2.2.1.1, grid size 104,104,104,
pixel 1, shown at level 0.107, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> artiax show #1.2.2 surfaces

> artiax particles #1.2.2 surfaceLevel -0.12246

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.2 models

> show #!1.2.2 models

> artiax particles #1.2.2 surfaceLevel -0.30686

> open /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/motl_M6_rf37_1.em

Opened motl_M6_rf37_1.em as #2, grid size 20,710,1, pixel 1, shown at step 1,
values float32  

> artiax attach #2 toParticleList #1.2.1

Opened motl_M6_rf37_1.em as #1.2.1.1.1, grid size 20,710,1, pixel 1, shown at
level 1.33e+03, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> open /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/motl_M6_rf37_1.em

Opened motl_M6_rf37_1.em as #2, grid size 20,710,1, pixel 1, shown at step 1,
values float32  

> artiax attach #2 toParticleList #1.2.1

Opened motl_M6_rf37_1.em as #1.2.1.1.1, grid size 20,710,1, pixel 1, shown at
level 1.33e+03, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> artiax particles #1.2.1 surfaceLevel 507.8736

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em

Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened M7_rf4_IR_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1,
shown at level 0.0905, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> artiax particles #1.2.1 surfaceLevel -0.13545

> lighting soft

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf18_bin4_20_symmetrized.em

Opened M7_rf18_bin4_20_symmetrized.em as #2, grid size 180,180,180, pixel 1,
shown at level 0.0656, step 1, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened M7_rf18_bin4_20_symmetrized.em as #1.2.2.1.1, grid size 180,180,180,
pixel 1, shown at level 0.0656, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> artiax show #1.2.2 surfaces

> hide #!1.2.1 models

> artiax particles #1.2.2 surfaceLevel -0.09289

> artiax particles #1.2.2 color 37,95,95,100

> artiax particles #1.2.2 surfaceLevel -0.08607

> show #!1.2.1 models

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.2 models

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf56_bin4_17.em

Opened M7_rf56_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.104, step 1, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened M7_rf56_bin4_17.em as #1.2.2.1.1, grid size 120,120,120, pixel 1, shown
at level 0.104, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> artiax show #1.2.2 surfaces

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf18_bin4_20_symmetrized.em

Opened M7_rf18_bin4_20_symmetrized.em as #2, grid size 180,180,180, pixel 1,
shown at level 0.0656, step 1, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened M7_rf18_bin4_20_symmetrized.em as #1.2.2.1.1, grid size 180,180,180,
pixel 1, shown at level 0.0656, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> artiax show #1.2.2 surfaces

> artiax particles #1.2.2 surfaceLevel -0.10652

> show #!1.2.2 models

> hide #!1.2.1 models

> artiax particles #1.2.2 surfaceLevel -0.0779

> show #!1.2.1 models

> hide #!1.2.2 models

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf56_bin4_17.em

Opened M7_rf56_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.104, step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened M7_rf56_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1, shown
at level 0.104, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> artiax particles #1.2.1 surfaceLevel -0.13775

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em

Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened M7_rf4_IR_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1,
shown at level 0.0905, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> artiax particles #1.2.1 surfaceLevel -0.12073

> artiax particles #1.2.1 surfaceLevel -0.10969

> artiax particles #1.2.1 surfaceLevel -0.13545

> hide #1.1 models

> hide #!1 models

> hide #!1.2 models

> hide #1.3 models

> hide #!1.2.1 models

> show #!1.2.1 models

> save /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/test1.mrc
> models #1.2.1.1.1

> vop resample #1.2.1

volume resample must specify onGrid option or spacing option  

> vop resample #1.2.1 onGrid #1.2

Opened M7_rf4_IR_bin4_17.em resampled as #2, grid size 120,120,120, pixel 1,
shown at step 1, values float32  
Opened M7_rf4_IR_bin4_17.em resampled as #3, grid size 180,180,180, pixel 1,
shown at step 1, values float32  

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> hide #!1.2.1 models

> hide #!1.2 models

> show #!2 models

> show #!3 models

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.1 models

> view orient

> hide #!3 models

> show #!3 models

> show #1.3 models

> close #3

> close #2

> show #!1.2.2 models

> hide #!1.2.2 models

> volume combine #1.2.1 method sum

Expected a density maps specifier or a keyword  

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em

Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32  

> close #2

> close #1.2.2.1.1

> close #1.2.1.1.1

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em

Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened M7_rf4_IR_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1,
shown at level 0.0905, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax particles #1.2.1 surfaceLevel -0.12441

> volume combine #2 method sum

Expected a density maps specifier or a keyword  

> volume combine #1.2 method sum

Expected a density maps specifier or a keyword  

> hide #!1.2.1 models

> volume #1.2.1.1.1 level -0.162

> view orient

> show #!1.2.1 models

> volume combine #1.2.1.1.1 method sum

Expected a density maps specifier or a keyword  

> volume #1.2.1.1.1 level -0.09708

> volume combine #1.2.1 method sum

Expected a density maps specifier or a keyword  

> export map

Unknown command: artiax export map  

> volume copy #1.2.1.1.1 coordinateSystem #1.2.1

Expected a keyword  

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em

Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32  

> volume copy #2 coordinateSystem #1.2.1

Expected a keyword  
0.202"">volume #4 level -0.202

> volume #4 color #aeafe7

> volume #4 level -0.2202

> volume #5 level -0.1815

> volume #4 level -0.2385

> volume #4 level -0.2124

> volume #18 level -0.1602

> volume #16 level -0.1474

> volume #16 level -0.1528

> volume #18 level -0.1459

> ui tool show ""Map Coordinates""

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_1.em

Opened M7_rf720_bin4_1.em as #19, grid size 140,140,140, pixel 1, shown at
level 0.17, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_2.em

Opened M7_rf720_bin4_2.em as #20, grid size 140,140,140, pixel 1, shown at
level 0.174, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_3.em

Opened M7_rf720_bin4_3.em as #21, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_4.em

Opened M7_rf720_bin4_4.em as #22, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_5.em

Opened M7_rf720_bin4_5.em as #23, grid size 140,140,140, pixel 1, shown at
level 0.174, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_6.em

Opened M7_rf720_bin4_6.em as #24, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_7.em

Opened M7_rf720_bin4_7.em as #25, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_8.em

Opened M7_rf720_bin4_8.em as #26, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_9.em

Opened M7_rf720_bin4_9.em as #27, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_10.em

Opened M7_rf720_bin4_10.em as #28, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_11.em

Opened M7_rf720_bin4_11.em as #29, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> hide #!18 models

> hide #!18-29 target m

> volume capFaces false

> show #!19 models

> hide #!19 models

> volume #29 level -0.2036

> volume #29 level -0.2054

> volume #28 level -0.1904

> close #28

> volume #27 level -0.2042

> close #27

> close #26

> close #25

> close #24

> close #23

> close #22

> close #21

> close #20

> close #19

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_13.em

Opened M7_rf720_bin4_13.em as #19, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_15.em

Opened M7_rf720_bin4_15.em as #20, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_17.em

Opened M7_rf720_bin4_17.em as #21, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_19.em

Opened M7_rf720_bin4_19.em as #22, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_21.em

Opened M7_rf720_bin4_21.em as #23, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> volume capFaces false

> hide #!19-23 target m

> volume #23 level -0.1845

> surface dust #23 size 10

> volume #23 level -0.1623

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder724/M7_rf724_bin4_21.em

Opened M7_rf724_bin4_21.em as #24, grid size 140,140,140, pixel 1, shown at
level 0.189, step 1, values float32  

> volume capFaces false

> volume #24 level -0.1711

> surface dust #24 size 10

> volume #24 level -0.1557

> volume #24 level -0.1711

> volume #23 level -0.1458

> volume #24 level -0.1557

> close #16-24,29

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_21.em

Opened M7_rf720_bin4_21.em as #16, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder721/M7_rf721_bin4_21.em

Opened M7_rf721_bin4_21.em as #17, grid size 140,140,140, pixel 1, shown at
level 0.124, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder722/M7_rf722_bin4_21.em

Opened M7_rf722_bin4_21.em as #18, grid size 140,140,140, pixel 1, shown at
level 0.134, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder723/M7_rf723_bin4_21.em

Opened M7_rf723_bin4_21.em as #19, grid size 140,140,140, pixel 1, shown at
level 0.128, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder724/M7_rf724_bin4_21.em

Opened M7_rf724_bin4_21.em as #20, grid size 140,140,140, pixel 1, shown at
level 0.189, step 1, values float32  

> volume capFaces false

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder725_new/M7_rf725_bin4_21.em

Opened M7_rf725_bin4_21.em as #21, grid size 140,140,140, pixel 1, shown at
level 0.191, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder726_new/M7_rf726_bin4_21.em

Opened M7_rf726_bin4_21.em as #22, grid size 140,140,140, pixel 1, shown at
level 0.134, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder727/M7_rf727_bin4_21.em

Opened M7_rf727_bin4_21.em as #23, grid size 140,140,140, pixel 1, shown at
level 0.159, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder728/M7_rf728_bin4_21.em

Opened M7_rf728_bin4_21.em as #24, grid size 140,140,140, pixel 1, shown at
level 0.141, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder729/M7_rf729_bin4_21.em

Opened M7_rf729_bin4_21.em as #25, grid size 140,140,140, pixel 1, shown at
level 0.204, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder730/M7_rf730_bin4_21.em

Opened M7_rf730_bin4_21.em as #26, grid size 140,140,140, pixel 1, shown at
level 0.188, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder731/M7_rf731_bin4_21.em

Opened M7_rf731_bin4_21.em as #27, grid size 140,140,140, pixel 1, shown at
level 0.124, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder732/M7_rf732_bin4_21.em

Opened M7_rf732_bin4_21.em as #28, grid size 140,140,140, pixel 1, shown at
level 0.141, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder733/M7_rf733_bin4_21.em

Opened M7_rf733_bin4_21.em as #29, grid size 140,140,140, pixel 1, shown at
level 0.129, step 1, values float32  

> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder734/M7_rf734_bin4_21.em

Opened M7_rf734_bin4_21.em as #30, grid size 140,140,140, pixel 1, shown at
level 0.198, step 1, values float32  

> volume capFaces false

> surface dust #16 size 10

> surface dust #17 size 10

> surface dust #18 size 10

> surface dust #19 size 10

> surface dust #20 size 10

> surface dust #21 size 10

> surface dust #22 size 10

> surface dust #23 size 10

> surface dust #24 size 10

> surface dust #25 size 10

> surface dust #26 size 10

> surface dust #27 size 10

> surface dust #28 size 10

> surface dust #29 size 10

> surface dust #30 size 10

> hide #!16-30 target m

> show #!30 models

> volume #30 level -0.146

> volume #28 level -0.1314

> volume #28 level -0.1153

> volume #26 level -0.1508

> volume #27 level -0.1317

> volume #29 level -0.1112

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> volume #25 level -0.1678

> volume #25 level -0.1339

> volume #24 level -0.0859

> volume #24 level -0.09677

> volume #24 color #9bd2d2

> volume #23 level -0.145

> volume #23 level -0.1203

> volume #23 color #dcdba5

> volume #22 level -0.09814

> volume #23 level -0.107

> volume #21 level -0.1549

> volume #21 color #89d589

> volume #21 level -0.1233

> volume #20 level -0.1309

> volume #20 level -0.1538

> volume #20 level -0.1481

> volume #20 level -0.1423

> volume #16 level -0.1328

> open /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/test1.mrc

Opened test1.mrc as #31, grid size 120,120,120, pixel 1, shown at level
0.0905, step 1, values float32  

> close #31


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

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

> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_rings/motl_M7_rf58_1_rings_per13n30_bin4_1.em

Opened motl_M7_rf58_1_rings_per13n30_bin4_1.em as #1, grid size 20,308,1,
pixel 1, shown at step 1, values float32  

> volume #1

> volume #1 style image

> volume #1 colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 9,153,0 imageMode orthoplanes

> volume #1 colorMode auto8 imageMode ""tilted slab"" tiltedSlabAxis
> -0.2485,-0.002018,0.9686 tiltedSlabOffset -3.17

> volume #1 colorMode opaque8 imageMode ""box faces""

> lighting soft

> ui tool show ""Side View""

> view orient

> close #1

> toolshed show

Downloading bundle ChimeraX_ArtiaX-0.6.0-py3-none-any.whl  
Installed ChimeraX-ArtiaX (0.6.0)  
Downloading bundle ChimeraX_ArtiaX-0.6.0-py3-none-any.whl  
Installed ChimeraX-ArtiaX (0.6.0)  
Replacing data format 'Artiatomi Motivelist' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX  
Replacing data format 'Generic Particle List' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX  
Replacing data format 'Dynamo Table' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'RELION STAR file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'RELION5 STAR file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'cryoET Data Portal' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'Coords file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'Copick Picks file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'PEET mod/csv' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX  
Replacing data format 'ArtiaX geometric model' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX  

Overriding existing toolbar provider for toolbar provider 'Launch' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Help' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'XY' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'XZ' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'YZ' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Clip' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Invert Contrast' in
bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Invert Selection'
in bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Sphere' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Line' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Surface' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Boundary' in bundle
'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Triangles From
Links' in bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Triangulate' in
bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Remove Selected' in
bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Create Mask' in
bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Volume to Geomodel'
in bundle 'ChimeraX-ArtiaX'  

Overriding existing toolbar provider for toolbar provider 'Geomodel to Volume'
in bundle 'ChimeraX-ArtiaX'  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
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: Mac14,7
      Model Number: Z16S000PCD/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 14 days, 29 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        EV2795:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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