![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#7391 assigned defect
ArtiaX: ValueError: Unknown class name 'MarkerSetPlus'
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000113397600 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 496 in swap_buffers
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 179 in draw
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 1300000,
"procLaunch" : "2022-08-03 14:52:39.8879 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "iMac17,1",
"procStartAbsTime" : 1286492997613872,
"coalitionID" : 39093,
"osVersion" : {
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"build" : "21F79",
"releaseType" : "User"
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"captureTime" : "2022-08-04 11:33:05.4014 -0400",
"incident" : "7E48CB5D-32EB-43D7-BD2A-9CBAF3EC5AA9",
"bug_type" : "309",
"pid" : 44975,
"procExitAbsTime" : 1360918348109716,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6851ABA1-0607-534C-AA87-A9AC45C1CD8B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2D4715BD-FA4F-0D39-E3B7-775AFCF69647",
"sip" : "disabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics kernel error: 0x1bf085f9\n"],
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"faultingThread" : 0,
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"arch" : "x86_64",
"base" : 4663664640,
"size" : 4997120,
"uuid" : "4969d1ff-28d9-3632-9358-784c5dec38c8",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4600963072,
"size" : 2818048,
"uuid" : "0a164d84-8b44-3f10-9065-1d0486c25a4b",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703249907712,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "f8e45ef9-9fd2-3331-bb1b-703d5dacdaf1",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1863"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703397720064,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3096576,
"uuid" : "04544f53-a387-3ac3-a85d-f8adfc0bc69e",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4541992960,
"CFBundleShortVersionString" : "1.4.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "9596eff5-d2be-396c-9c4e-6177235c3dae",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.4.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4616974336,
"size" : 442368,
"uuid" : "b70ce1ec-b902-3852-8268-05de00bfa8d5",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4684021760,
"size" : 63488000,
"uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5030895616,
"size" : 165068800,
"uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5614596096,
"size" : 147456,
"uuid" : "c77aa6bd-464f-397d-9361-6e5f3450a851",
"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numexpr\/interpreter.cpython-39-darwin.so",
"name" : "interpreter.cpython-39-darwin.so"
}
],
"sharedCache" : {
"base" : 140703246336000,
"size" : 15220686848,
"uuid" : "398acfb4-57f6-31e0-bc82-e9959e5c92ce"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=18.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=18.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 2276K 74 \nColorSync 236K 28 \nCoreAnimation 9708K 82 \nCoreGraphics 12K 2 \nCoreUI image data 5168K 40 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 13.9G 1818 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 116K 29 \nStack 142.7M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 4.6G 378 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 58.5M 742 \n__DATA_CONST 31.4M 350 \n__DATA_DIRTY 1659K 218 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 682.9M 189 \n__TEXT 815.5M 723 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 535.6M 86 \nshared memory 2984K 29 \n=========== ======= ======= \nTOTAL 20.9G 4855 \nTOTAL, minus reserved VM space 20.9G 4855 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61af99aeda72d16a4beb7756",
"factorPackIds" : {
"SIRI_DIALOG_ASSETS" : "62e81c317613a1631383416b"
},
"deploymentId" : 240000296
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show ArtiaX
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened TS_001_rec.mrc as #1.1.1, grid size 1023,1440,350, pixel
8.48,8.48,8.48, shown at level 22.1, step 1, values int16
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/Load_script_with_AP_PE_tRNA/refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.star"
> format star
Opened Particle list
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.star
with 4721 particles.
> ui tool show "Volume Viewer"
> volume #1.1.1 region 0,0,172,1022,1439,172 step 1 showOutlineBox true
> imageMode "full region"
> volume #1.1.1 level -55.94,0 level -3.441,0.6538 level 57.89,1
> ui tool show "Map Coordinates"
> artiax tomo #1.1.1 slice 178
> artiax particles #1.2.1 originScaleFactor 1.0
> artiax view xy
> volume #1.1.1 imageMode "full region"
> artiax particles #1.2.1 originScaleFactor 2.12
> artiax view xy
> artiax tomo #1.1.1 pixelSize 8.479997174364614
> artiax view xy
> volume #1.1.1 imageMode "full region"
> artiax tomo #1.1.1 pixelSize 2.12
> artiax view xy
> artiax tomo #1.1.1 pixelSize 2.12
> artiax view xy
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> artiax particles #1.2.1 originScaleFactor 8.48
> artiax view xy
> artiax particles #1.2.1 originScaleFactor 8.48
> artiax view xy
> artiax particles #1.2.1 originScaleFactor 8.48
> artiax view xy
> artiax particles #1.2.1 originScaleFactor 2.12
> artiax view xy
> volume #1.1.1 imageMode "full region"
> artiax particles #1.2.1 originScaleFactor 2.12
> artiax view xy
> artiax tomo #1.1.1 pixelSize 2.12
> artiax view xy
> artiax tomo #1.1.1 pixelSize 2.12
> artiax view xy
> volume #1.1.1 imageMode "full region"
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> volume #1.1.1 imageMode "full region"
> help help:user/tools/artiax_options.html
Pixelsize needs to be > 0.
> artiax particles #1.2.1 transScaleFactor 1.0
> artiax view xy
> artiax particles #1.2.1 originScaleFactor 8.48
> artiax view xy
> toolshed install ArtiaX
ChimeraX-ArtiaX (0.1) is already installed
> artiax particles #1.2.1 originScaleFactor 8.48
> artiax view xy
Pixelsize needs to be > 0.
> artiax particles #1.2.1 transScaleFactor 1.0
> artiax view xy
Pixelsize needs to be positive and non-zero.
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> volume #1.1.1 imageMode "full region"
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/maps_from_relion/refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_L1_stalk_away_bin1_job245.mrc"
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_L1_stalk_away_bin1_job245.mrc
as #2, grid size 256,256,256, pixel 2.12, shown at level 4.5, step 1, values
float32
> artiax attach #2 toParticleList #1.2.1
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_L1_stalk_away_bin1_job245.mrc
as #1.2.1.1.1, grid size 256,256,256, pixel 2.12, shown at level 4.5, step 1,
values float32
> volume #1.2.1.1.1 capFaces false
> artiax particles #1.2.1 surfaceLevel 3.48349
> artiax particles #1.2.1 originScaleFactor 2.12
> artiax view xy
> artiax particles #1.2.1 transScaleFactor 8.48
> artiax view xy
> artiax particles #1.2.1 transScaleFactor 1.0
> artiax view xy
Please enter a valid number for the pixelsize.
> artiax particles #1.2.1 transScaleFactor 1.0
> artiax view xy
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> artiax particles #1.2.1 transScaleFactor 8.48
> artiax view xy
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> volume #1.1.1 region 0,0,97,1022,1439,97
> volume #1.1.1 region 0,0,340,1022,1439,340
> volume #1.1.1 region 0,0,349,1022,1439,349
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> artiax tomo #1.1.1 pixelSize 8.48
> artiax view xy
> volume #1.2.1.1.1 style image region 0,0,127,255,255,127 step 1
> showOutlineBox true
> volume #1.1.1 imageMode "full region"
> volume #1.2.1.1.1 region 0,0,0,255,255,255 step 1
> volume #1.2.1.1.1 style surface
> volume #1.2.1.1.1 change image level -0.5376,0 level 5.698,0.8 level 8.976,1
> volume #1.2.1.1.1 showOutlineBox false
> volume #1.1.1 showOutlineBox false
> volume #1.1.1 showOutlineBox true
> volume #1.1.1 region 0,0,0,1022,1439,349 step 4
> volume #1.1.1 region 0,0,172,1022,1439,172 step 1
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/Load_script_with_AP_PE_tRNA/refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216_bin4.mrc"
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216_bin4.mrc
as #2, grid size 64,64,64, pixel 8.48, shown at level 4.46, step 1, values
float32
> artiax attach #2 toParticleList #1.2.1
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216_bin4.mrc
as #1.2.1.1.1, grid size 64,64,64, pixel 8.48, shown at level 4.46, step 1,
values float32
> volume #1.2.1.1.1 capFaces false
> artiax particles #1.2.1 surfaceLevel 3.49871
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/Load_script_with_AP_PE_tRNA/refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.star"
> format star
Opened Particle list
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.star
with 4721 particles.
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/maps_from_relion/refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.mrc"
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.mrc
as #2, grid size 256,256,256, pixel 2.12, shown at level 4.54, step 1, values
float32
> artiax attach #2 toParticleList #1.2.2
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_bin1_job216.mrc
as #1.2.2.1.1, grid size 256,256,256, pixel 2.12, shown at level 4.54, step 1,
values float32
> volume #1.2.2.1.1 capFaces false
> artiax particles #1.2.2 surfaceLevel 5.82788
> artiax particles #1.2.2 surfaceLevel 2.82558
> volume #1.1.1 region 0,0,272,1022,1439,272
> volume #1.1.1 region 0,0,104,1022,1439,104
> hide #!1.2.2 models
> show #!1.2.2 models
> artiax particles #1.2.2 originScaleFactor 2.12
> artiax view xy
> 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
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.2 models
> show #!1.2.1 models
> artiax particles #1.2.2 surfaceLevel 3.37145
> artiax particles #1.2.1 surfaceLevel 3.252
> artiax particles #1.2.1 surfaceLevel 3.12864
> hide #!1.2.2 models
> show #!1.2.2 models
> artiax tomo #1.1.1 contrastCenter -11.1378
> artiax tomo #1.1.1 contrastCenter -26.31496
> artiax particles #1.2.2 surfaceLevel 2.77099
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> volume #1.2.2.1.1 level 5.124
> show #!1.2.2 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
> show #!1.2.2 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
> show #!1.2.2 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
> show #!1.2.2 models
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/Load_script_with_AP_PE_tRNA_AP_shifted_right/refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237.star"
> format star
Opened Particle list
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237.star
with 2352 particles.
> artiax particles #1.2.1 originScaleFactor 2.12
> artiax view xy
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237.mrc
as #2, grid size 256,256,256, pixel 2.12, shown at level 4.53, step 1, values
float32
> artiax attach #2 toParticleList #1.2.1
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_withAP_PE_tRNA_shifted_right_bin1_job237.mrc
as #1.2.1.1.1, grid size 256,256,256, pixel 2.12, shown at level 4.53, step 1,
values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel 3.2813
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/maps_from_relion/refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257.star"
> format star
Opened Particle list
refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257.star
with 1277 particles.
> artiax particles #1.2.3 originScaleFactor 2.12
> artiax view xy
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257.mrc
as #2, grid size 256,256,256, pixel 2.12, shown at level 4.57, step 1, values
float32
> artiax attach #2 toParticleList #1.2.3
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_bin1_job257.mrc
as #1.2.3.1.1, grid size 256,256,256, pixel 2.12, shown at level 4.57, step 1,
values float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax particles #1.2.3 surfaceLevel 4.2258
> artiax particles #1.2.3 surfaceLevel 3.44895
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/maps_from_relion/refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267.star"
> format star
Opened Particle list
refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267.star
with 765 particles.
> artiax particles #1.2.4 originScaleFactor 2.12
> artiax view xy
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267.mrc
as #2, grid size 256,256,256, pixel 2.12, shown at level 4.43, step 1, values
float32
> artiax attach #2 toParticleList #1.2.4
Opened
refine_after_frame_CTF_withmask_after_focus_noalign_with_PPtRNA_L1_stalk_back_bin1_job267.mrc
as #1.2.4.1.1, grid size 256,256,256, pixel 2.12, shown at level 4.43, step 1,
values float32
> volume #1.2.4.1.1 capFaces false
> artiax show #1.2.4 surfaces
> artiax particles #1.2.4 surfaceLevel 3.01316
> artiax particles #1.2.4 surfaceLevel 3.27631
> volume #1.2.4.1.1 level 4.427
> volume #1.2.4.1.1 level 4.451
> volume #1.2.4.1.1 level 4.905
> artiax particles #1.2.2 surfaceLevel 3.91733
> artiax particles #1.2.2 surfaceLevel 3.97191
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.3 models
> show #!1.2.3 models
> hide #!1.2.3 models
> hide #!1.2.4 models
> show #!1.2.4 models
> show #!1.2.3 models
> artiax particles #1.2.2 surfaceLevel 2.88017
> artiax particles #1.2.2 surfaceLevel 1.89759
> artiax particles #1.2.2 surfaceLevel 3.09852
> artiax tomo #1.1.1 slice 1
> volume #1.1.1 imageMode "full region"
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.2 models
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/TS_001_all_classes.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
Populating font family aliases took 319 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> show #!1.2.2 models
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/TS_001_all_classes.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_AP_PE_tRNA_bin1_job216.em"
> partlist #1.2.2
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_AP_PE_tRNA_shifted_right_bin1_job237.em"
> partlist #1.2.1
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_PPtRNA_bin1_job257.em"
> partlist #1.2.3
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_PPtRNA_L1_stalk_back_bin1_job267.em"
> partlist #1.2.4
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/TS_001_all_classes.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> volume #1.1.1 region 0,0,53,1022,1439,53
> volume #1.1.1 region 0,0,142,1022,1439,142
> volume #1.1.1 region 0,0,154,1022,1439,154
> volume #1.1.1 region 0,0,118,1022,1439,118
> volume #1.1.1 region 0,0,133,1022,1439,133
> volume #1.1.1 region 0,0,257,1022,1439,257
> volume #1.1.1 region 0,0,287,1022,1439,287
> volume #1.1.1 region 0,0,349,1022,1439,349
> volume #1.1.1 region 0,0,320,1022,1439,320
> volume #1.1.1 region 0,0,192,1022,1439,192
> volume #1.1.1 region 0,0,221,1022,1439,221
> volume #1.1.1 region 0,0,238,1022,1439,238
> volume #1.1.1 region 0,0,240,1022,1439,240
> volume #1.1.1 region 0,0,214,1022,1439,214
> volume #1.1.1 region 0,0,208,1022,1439,208
> volume #1.1.1 region 0,0,212,1022,1439,212
> volume #1.1.1 region 0,0,232,1022,1439,232
> volume #1.1.1 region 0,0,215,1022,1439,215
> volume #1.1.1 region 0,0,0,1022,1439,0
> volume #1.1.1 region 0,0,227,1022,1439,227
> volume #1.1.1 region 0,0,222,1022,1439,222
> volume #1.1.1 region 0,0,242,1022,1439,242
> volume #1.1.1 region 0,0,213,1022,1439,213
> volume #1.1.1 region 0,0,242,1022,1439,242
> volume #1.1.1 region 0,0,233,1022,1439,233
> volume #1.1.1 region 0,0,210,1022,1439,210
> volume #1.1.1 region 0,0,215,1022,1439,215
> volume #1.1.1 region 0,0,216,1022,1439,216
> volume #1.1.1 region 0,0,218,1022,1439,218
> volume #1.1.1 region 0,0,201,1022,1439,201
> volume #1.1.1 region 0,0,211,1022,1439,211
> volume #1.1.1 region 0,0,210,1022,1439,210
> volume #1.1.1 region 0,0,190,1022,1439,190
> volume #1.1.1 region 0,0,196,1022,1439,196
> volume #1.1.1 region 0,0,159,1022,1439,159
> volume #1.1.1 region 0,0,155,1022,1439,155
> volume #1.1.1 region 0,0,192,1022,1439,192
> volume #1.1.1 region 0,0,188,1022,1439,188
> volume #1.1.1 region 0,0,206,1022,1439,206
> volume #1.1.1 region 0,0,211,1022,1439,211
> volume #1.1.1 region 0,0,210,1022,1439,210
> volume #1.1.1 region 0,0,201,1022,1439,201
> volume #1.1.1 region 0,0,210,1022,1439,210
> volume #1.1.1 region 0,0,200,1022,1439,200
> volume #1.1.1 region 0,0,176,1022,1439,176
> volume #1.1.1 region 0,0,186,1022,1439,186
> volume #1.1.1 region 0,0,208,1022,1439,208
> volume #1.1.1 region 0,0,201,1022,1439,201
> volume #1.1.1 region 0,0,191,1022,1439,191
> volume #1.1.1 region 0,0,189,1022,1439,189
> volume #1.1.1 region 0,0,206,1022,1439,206
> open help:user/artiax_index.html
Opened help:user/artiax_index.html
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/gfdghfdhgfdghf.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_AP_PE_tRNA_bin1_job216.em"
Opened With_AP_PE_tRNA_bin1_job216.em as #2, grid size 20,4721,1, pixel
8.08e+05, shown at step 1, values float32
> volume #2 level -0.07108,0 level 3790,0.8 level 5632,1
> volume #2 level 150.1,0.1692 level 3790,0.8 level 5632,1
> volume #2 level -57.82,0.6308 level 3790,0.8 level 5632,1
> volume #2
> volume #2 style image showOutlineBox true
> close #2
> preset artiax "artiax default"
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> preset artiax "artiax default"
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> ui tool show "Marker Placement"
> ui tool show "Model Panel"
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> show #1.1.1.1 models
> hide #1.1.1.1 models
> show #1.1.1.1 models
> hide #1.1.1.1 models
> show #1.1.1.1 models
> ui mousemode right "delete markers"
> help help:user/tools/markerplacement.html
> ui tool show "Model Panel"
> close #2
> select add #1.1
4 models selected
> select subtract #1.1
Nothing selected
> hide #!1.1.1 models
> show #!1.1.1 models
> toolshed install ArtiaX
ChimeraX-ArtiaX (0.1) is already installed
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.1.1 models
> show #!1.1.1 models
> ui tool show "Volume Viewer"
> hide #!1.2.2 models
> show #!1.2.2 models
> ui tool show "Side View"
> view
> ui tool show "Volume Viewer"
> ui autostart true "Volume Viewer"
> volume #1.1.1 level 25.82
> volume #1.1.1 level 17.06
> volume #1.1.1 style image
> volume #1.1.1 level -11.9,0.3385 level -26.31,0.5 level 30.6,1
> volume #1.1.1 level -11.9,0.3385 level -51.34,0.007692 level 30.6,1
> volume #1.1.1 level -9.396,0.5231 level -51.34,0.007692 level 30.6,1
> volume #1.1.1 level -13.15,0.5538 level -51.34,0.007692 level 30.6,1
> cd "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes"
Current working directory is: /Users/jingyu/Desktop/Image
processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/jhgjg.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/maps_from_relion/asdfdsaf.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_AP_PE_tRNA_bin1_job216.star"
> partlist #1.2.2
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_AP_PE_tRNA_shifted_right_bin1_job237.star"
> partlist #1.2.1
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_PPtRNA_bin1_job257.star"
> partlist #1.2.3
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/With_PPtRNA_L1_stalk_back_bin1_job267.star"
> partlist #1.2.4
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/dsfadsf.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/sdfaf.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/TS_001_all_classes/vcbgrt.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/jingyu/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.3 models
> show #!1.2.3 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> 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
> volume #1.1.1 region 0,0,22,1022,1439,22
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> open
> /Users/jingyu/Downloads/ArtiaX_supplementary_data_1/myco_script_demo.cxc
> cd /home/Group/Share/ArtiaX/demo
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> open "/Users/jingyu/Desktop/Image
> processing/RNAgranules_tomo/subtomo2Chimera/maps_from_relion/refine_after_no_align_with_only_60S_bin2_job052.star"
> format star
Opened Particle list refine_after_no_align_with_only_60S_bin2_job052.star with
7617 particles.
> artiax particles #1.2.5 originScaleFactor 1.0
> artiax view xy
> artiax particles #1.2.5 originScaleFactor 2.12
> artiax view xy
Opened refine_after_no_align_with_only_60S_bin2_job052.mrc as #2, grid size
128,128,128, pixel 4.24, shown at level 4.19, step 1, values float32
> artiax attach #2 toParticleList #1.2.5
Opened refine_after_no_align_with_only_60S_bin2_job052.mrc as #1.2.5.1.1, grid
size 128,128,128, pixel 4.24, shown at level 4.19, step 1, values float32
> volume #1.2.5.1.1 capFaces false
> artiax show #1.2.5 surfaces
> artiax particles #1.2.5 surfaceLevel 4.16217
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> show #!1.2.5 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
> show #!1.2.2 models
> hide #!1.2.5 models
> show #!1.2.5 models
> artiax particles #1.2.5 surfaceLevel 2.65567
> artiax particles #1.2.5 surfaceLevel 2.95697
> artiax particles #1.2.5 surfaceLevel 3.94304
> artiax particles #1.2.5 surfaceLevel 2.98436
> artiax particles #1.2.5 surfaceLevel 2.92958
> volume #1.1.1 region 0,0,157,1022,1439,157
> volume #1.1.1 region 0,0,177,1022,1439,177
> volume #1.1.1 region 0,0,150,1022,1439,150
> volume #1.1.1 region 0,0,158,1022,1439,158
> hide #!1.2.5 models
> volume #1.1.1 region 0,0,153,1022,1439,153
> show #!1.2.5 models
> volume #1.1.1 region 0,0,139,1022,1439,139
> volume #1.1.1 region 0,0,123,1022,1439,123
> hide #!1.2.5 models
> show #!1.2.5 models
> hide #!1.2.5 models
> volume #1.1.1 region 0,0,150,1022,1439,150
> show #!1.2.5 models
> volume #1.1.1 region 0,0,0,1022,1439,349 step 4
> volume #1.1.1 region 0,0,0,1022,1439,349 step 1 colorMode opaque8 imageMode
> "box faces"
> volume #1.1.1 color #f4f4f4 color white color white
> volume #1.1.1 style surface
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon R9 M395 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 451.120.7.0.0
OS Loader Version: 540.120.3~6
SMC Version (system): 2.34f3
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 15 days 18:02
Graphics/Displays:
AMD Radeon R9 M395:
Chipset Model: AMD Radeon R9 M395
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x6920
Revision ID: 0x0001
ROM Revision: 113-C905AA-799
VBIOS Version: 113-C905A1-007
EFI Driver Version: 01.00.799
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.1
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
pandas: 1.4.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
starfile: 0.4.11
suds-community: 1.0.0
superqt: 0.3.3
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
typing-extensions: 4.3.0
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (5)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics kernel error |
comment:2 by , 3 years ago
| Summary: | Graphics kernel error → Graphics crash, macOS 12.4, AMD Radeon R9 M395 |
|---|
Apple graphics driver crash.
But there are also numerous ArtiaX tracebacks before the crash that we should direct to Utz Ermel the ArtiaX developer.
comment:3 by , 3 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
| Summary: | Graphics crash, macOS 12.4, AMD Radeon R9 M395 → ArtiaX: ValueError: Unknown class name 'MarkerSetPlus' |
Hi Utz,
This is a ChimeraX bug report where ArtiaX is throwing some errors that you may want to look at and fix. This report ended in a crash unrelated to ArtiaX due to unstable Mac graphics drivers. So just check out the tracebacks. You can respond to this email to put comments on this ChimeraX ticket. You won't be able to close the ticket without getting an account with us. We can get you an account if you like, or you can just tell me (by sending email reply) and I will close it.
Tom
follow-up: 4 comment:4 by , 3 years ago
Hi Tom, thank you for letting me know about this, I will also mirror the issue on the ArtiaX github repository. This one seems related to ArtiaX not supporting saving to chimerax session files at the moment. Best, Utz Quoting ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>:
follow-up: 5 comment:5 by , 3 years ago
Thanks. When an error occurs in ChimeraX a error message appears with a Report Bug button, and if they press that a bug report is automatically made in our ChimeraX bug database. We assign those bugs to the responsible developer. Unfortunately we have no way of automatically redirecting those bugs to your Github issues.
Note:
See TracTickets
for help on using tickets.
Was using 20.9GB at the time.