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#17188 closed defect (not a bug)

ArtiaX: Unknown class name 'MarkerSetPlus'

Reported by:	chimerax-bug-report@…	Owned by:	Utz Ermel
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

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

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> open
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_18.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_19.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_20.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_21.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_22.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_23.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_24.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_25.em
> V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_26.em
> format motl

Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_18.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_19.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_20.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_21.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_22.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_23.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_24.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_25.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
V:/chzimmer/2022-09-01_chzimmer_tomo_DT2_1_DT2_4_TH2O11_4/TT4/warp/relion/bin1.27/STOPGAP_mr/RNA_cl_5runs_mr1/Splitmotls/Hibernating_vs_nonhibernating_26.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list Hibernating_vs_nonhibernating_18.em with 161 particles.  
Opened Particle list Hibernating_vs_nonhibernating_19.em with 261 particles.  
Opened Particle list Hibernating_vs_nonhibernating_20.em with 27 particles.  
Opened Particle list Hibernating_vs_nonhibernating_21.em with 392 particles.  
Opened Particle list Hibernating_vs_nonhibernating_22.em with 102 particles.  
Opened Particle list Hibernating_vs_nonhibernating_23.em with 22 particles.  
Opened Particle list Hibernating_vs_nonhibernating_24.em with 374 particles.  
Opened Particle list Hibernating_vs_nonhibernating_25.em with 1 particles.  
Opened Particle list Hibernating_vs_nonhibernating_26.em with 332 particles.  

> hide #!1.2.9 models

> hide #!1.2.8 models

> hide #!1.2.7 models

> hide #!1.2.6 models

> hide #!1.2.4 models

> hide #!1.2.3 models

> hide #!1.2.5 models

> hide #!1.2.2 models

> artiax particles #1.2.9 radius 47.37365

> artiax particles #1.2.9 radius 25.0875

set axis size 13.60676  
13.60676  
['.arrow', '0', '0', '0', '13.60676', '0', '0', '0.9071173333333333',
'3.6284693333333333']  
set axis size 12.25608  
12.25608  
['.arrow', '0', '0', '0', '12.25608', '0', '0', '0.817072', '3.268288']  
set axis size 9.55473  
9.55473  
['.arrow', '0', '0', '0', '9.55473', '0', '0', '0.6369819999999999',
'2.5479279999999997']  
set axis size 5.5027  
5.5027  
['.arrow', '0', '0', '0', '5.5027', '0', '0', '0.36684666666666665',
'1.4673866666666666']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.9 axesSize 0.1

set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.9 axesSize 0.1

> artiax particles #1.2.1 radius 10.0

set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.1 axesSize 0.1

> artiax particles #1.2.1 radius 19.6848

161 atoms, 161 residues, atom cross_correlation range 0.23 to 0.993  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 cross_correlation palette redgreen minValue
> 0.2295919954776764 maxValue 0.9927510023117065 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 25 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue
> 1.9347826086956523 maxValue 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 6 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue
> 1.9347826086956523 maxValue 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 13 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 1 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 91 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.999
> maxValue 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 16 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue
> 1.1702898550724639 maxValue 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 45 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue
> 1.1702898550724639 maxValue 2.0 transparency 0.0

161 atoms, 161 residues, atom class_number range 1 to 2  
[Repeated 13 time(s)]

> artiax colormap #1.2.1.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

> artiax particles #1.2.2 radius 10.0

set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.2 axesSize 0.1

261 atoms, 261 residues, atom cross_correlation range 0.192 to 0.991  
[Repeated 1 time(s)]

> artiax colormap #1.2.2.3 cross_correlation palette redgreen minValue
> 0.1921209990978241 maxValue 0.990676999092102 transparency 0.0

261 atoms, 261 residues, atom class_number range 1 to 2  
[Repeated 1 time(s)]

> artiax colormap #1.2.2.3 class_number palette redgreen minValue 1.0 maxValue
> 2.0 transparency 0.0

> show #!1.2.2 models

> hide #!1.2.1 models

> artiax particles #1.2.1 radius 20.0

> artiax particles #1.2.2 radius 20.0

Opened 019_corrected.mrc as #1.1.1, grid size 512,512,250, pixel 1, shown at
level 0.186, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

Opened 024_corrected.mrc as #1.1.2, grid size 512,512,250, pixel 1, shown at
level 0.177, step 1, values float32  

> artiax tomo #1.1.2 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #1.1.2 pixelSize 1.0

> artiax view xy

> artiax tomo #1.1.1 pixelSize 12.48

> artiax view xy

> artiax tomo #1.1.1 pixelSize 12.48

> artiax view xy

set axis size 28.5  
28.5  
['.arrow', '0', '0', '0', '28.5', '0', '0', '1.9', '7.6']  

> artiax particles #1.2.2 originScaleFactor 1.9

> artiax view xy

> artiax particles #1.2.2 radius 35.21757

> artiax tomo #1.1.1 slice 142

> artiax tomo #1.1.1 slice 121

> volume #1.1.1 level -2.709,0 level -0.5058,0.5 level 1.042,1

> volume #1.1.1 level -2.709,0 level -0.6013,0.5385 level 1.042,1

> volume #1.1.1 level -2.709,0 level -0.6013,0.5385 level 0.4687,0.9077

> volume #1.1.1 region 0,0,124,511,511,124 step 1 showOutlineBox true
> imageMode "full region"

> volume #1.1.1 region 0,0,0,511,511,249 step 2

> volume #1.1.1 region 0,0,0,511,511,249 step 2 imageMode "tilted slab"
> tiltedSlabAxis 0.1033,-0.3347,0.9366 tiltedSlabOffset 556.9
> tiltedSlabPlaneCount 25

> volume #1.1.1 tiltedSlabAxis 0.1231,-0.1189,0.9852 tiltedSlabOffset 1172

> volume #1.1.1 tiltedSlabAxis 0.1972,-0.03281,0.9798 tiltedSlabOffset 1675

> volume #1.1.1 tiltedSlabAxis -0.09332,-0.3145,0.9447 tiltedSlabOffset -193.4

> volume #1.1.1 tiltedSlabAxis -0.1461,0.09859,0.9844 tiltedSlabOffset 2117

> volume #1.1.1 step 1

> volume #1.1.1 colorMode opaque8 orthoplanes xyz positionPlanes 255,255,124
> imageMode orthoplanes

> volume #1.1.1 region 0,0,124,511,511,124 step 1 colorMode auto8 imageMode
> "full region"

> volume #1.1.1 region 0,0,0,511,511,249 step 1

> volume #1.1.1 region 0,0,0,511,511,249 step 1 imageMode "tilted slab"
> tiltedSlabAxis -0.4158,-0.2461,0.8755 tiltedSlabOffset -1062
> tiltedSlabPlaneCount 50

> close #1.1.1

> close #1.1.2

Opened 019_corrected.mrc as #1.1.1, grid size 512,512,250, pixel 1, shown at
level 0.186, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> open help:user/artiax_index.html

Opened help:user/artiax_index.html  

> artiax tomo #1.1.1 pixelSize 12.48

> artiax view xy

> artiax tomo #1.1.1 pixelSize 12.48

> artiax view xy

> volume #1.1.1 tiltedSlabAxis -0.02575,0.0003051,0.9997 tiltedSlabOffset 1425

> volume #1.1.1 tiltedSlabAxis -0.01673,0.1073,0.9941 tiltedSlabOffset 1787

> volume #1.1.1 tiltedSlabAxis -0.2242,-0.02984,0.9741 tiltedSlabOffset 338.6

> volume #1.1.1 tiltedSlabAxis -0.223,-0.06736,0.9725 tiltedSlabOffset 221

> volume #1.1.1 tiltedSlabAxis -0.2142,-0.0683,0.9744 tiltedSlabOffset 248.2

> volume #1.1.1 tiltedSlabAxis -0.1391,-0.1001,0.9852 tiltedSlabOffset 183.3

> volume #1.1.1 tiltedSlabAxis -0.2182,-0.0612,0.974 tiltedSlabOffset 129.1

> artiax tomo #1.1.1 slice 205

> view orient

[Repeated 1 time(s)]

> artiax tomo #1.1.1 slice 192

> save /ArtiaX_testsession.cxs includeMaps true

[Errno 13] Permission denied: '/ArtiaX_testsession.cxs.28036.tmp'  

> save C:/Users/zimmerli/Desktop/ArtiaxtEST.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\zimmerli\AppData\Local\UCSF\ChimeraX\1.7\Python311\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000002143DA41D90> ->
<chimerax.atomic.molobject.Atom object at 0x000002145123CD50> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\zimmerli\AppData\Local\UCSF\ChimeraX\1.7\Python311\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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000002143DA41D90> ->
<chimerax.atomic.molobject.Atom object at 0x000002145123CD50> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> toolshed show

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

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

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

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

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

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

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

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

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

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

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

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

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

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

> save C:/Users/zimmerli/Desktop/TESTS.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\zimmerli\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
from .options_window import OptionsWindow  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000002143DA41D90> ->
<chimerax.atomic.molobject.Atom object at 0x000002145123CD50> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\zimmerli\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
from .options_window import OptionsWindow  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000002143DA41D90> ->
<chimerax.atomic.molobject.Atom object at 0x000002145123CD50> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> artiax start

> open help:user/artiax_index.html

Opened help:user/artiax_index.html  

> save test.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\zimmerli\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
from .options_window import OptionsWindow  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000002143DA41D90> ->
<chimerax.atomic.molobject.Atom object at 0x000002145123CD50> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, 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 "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\state.py",
line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\zimmerli\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
from .options_window import OptionsWindow  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000002143DA41D90> ->
<chimerax.atomic.molobject.Atom object at 0x000002145123CD50> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 23.10.24.17.240703
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 21CGS0LG00
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 33,038,872,576
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 PRO 6850U with Radeon Graphics     
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    annotated-types: 0.7.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    pandas: 2.2.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 15.0.1
    pycollada: 0.7.2
    pydantic: 2.10.6
    pydantic-core: 2.27.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    starfile: 0.5.6
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.12.2
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 7 months ago

Component:	Unassigned → Third Party
Owner:	set to Utz Ermel
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ArtiaX: Unknown class name 'MarkerSetPlus'

comment:2 by pett, 7 months ago

Resolution:	→ not a bug
Status:	assigned → closed

User upgraded to ArtiaX 0.6 in the middle of the session, but needed to restart.

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