id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
7391	ArtiaX: ValueError: Unknown class name 'MarkerSetPlus'	chimerax-bug-report@…	Utz Ermel	"{{{
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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    ""size"" : 655360,
    ""uuid"" : ""009cdea9-f1bc-35e0-bf0e-099d3df37399"",
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    ""name"" : ""libqcocoa.dylib""
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  {
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    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui"",
    ""name"" : ""QtGui""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4612161536,
    ""size"" : 1474560,
    ""uuid"" : ""3f690a6f-eda7-3d60-ab04-013371e5bf30"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtGui.abi3.so"",
    ""name"" : ""QtGui.abi3.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4546813952,
    ""CFBundleShortVersionString"" : ""3.9.11, (c) 2001-2021 Python Software Foundation."",
    ""CFBundleIdentifier"" : ""org.python.python"",
    ""size"" : 2527232,
    ""uuid"" : ""ef9cc1f4-5991-3213-9a9e-e68c578b6c1b"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python"",
    ""name"" : ""Python"",
    ""CFBundleVersion"" : ""3.9.11""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
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    ""size"" : 1589248,
    ""uuid"" : ""e1eca899-9707-3319-ac6c-d8028378fb9a"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so"",
    ""name"" : ""QtCore.abi3.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4651282432,
    ""size"" : 5226496,
    ""uuid"" : ""97d356c9-7652-3ff7-be10-198e30670243"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore"",
    ""name"" : ""QtCore""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
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    ""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"",
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    ""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""
  },
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    ""source"" : ""P"",
    ""arch"" : ""x86_64h"",
    ""base"" : 140703249907712,
    ""CFBundleShortVersionString"" : ""6.9"",
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    ""size"" : 5255168,
    ""uuid"" : ""f8e45ef9-9fd2-3331-bb1b-703d5dacdaf1"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
    ""CFBundleVersion"" : ""1863""
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    ""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""
  },
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    ""uuid"" : ""9596eff5-d2be-396c-9c4e-6177235c3dae"",
    ""path"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX"",
    ""name"" : ""ChimeraX"",
    ""CFBundleVersion"" : ""1.4.0.0""
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    ""path"" : ""\/usr\/lib\/dyld"",
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    ""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""
  },
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    ""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"",
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    ""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""
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],
  ""sharedCache"" : {
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  ""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"" : {
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    ""queue"" : ""com.apple.main-thread""
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},
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  ""rollouts"" : [
    {
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      ""factorPackIds"" : {
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      },
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}
===== 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

}}}
"	defect	assigned	normal		Graphics				Tom Goddard				all	ChimeraX