ArtiaX session save: Unknown class name 'MarkerSetPlus'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.5rc202210282349 (2022-10-28 23:49:04 UTC)
Description
saving a session with results from Artiax seems not to be working

Log:
UCSF ChimeraX version: 1.5rc202210282349 (2022-10-28)  
© 2016-2022 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

  
Opened 20220318_tomo44.mrc_17.36Apx.mrc as #1.1.1, grid size 500,712,376,
pixel 17.4,17.4,17.4, shown at level 0.146, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> open /Users/juliette/Desktop/40S_files/starfiles/tomo44_40s_eif5b_data.star
> /Users/juliette/Desktop/40S_files/starfiles/tomo44_40s_empty_data.star
> /Users/juliette/Desktop/40S_files/starfiles/tomo44_43s_data.star
> /Users/juliette/Desktop/40S_files/starfiles/tomo44_43s_eif4g_data.star
> /Users/juliette/Desktop/40S_files/starfiles/tomo44_60s_data.star
> /Users/juliette/Desktop/40S_files/starfiles/tomo44_80s_data.star format star

Summary of feedback from opening
/Users/juliette/Desktop/40S_files/starfiles/tomo44_40s_eif5b_data.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/juliette/Desktop/40S_files/starfiles/tomo44_40s_empty_data.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/juliette/Desktop/40S_files/starfiles/tomo44_43s_data.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/juliette/Desktop/40S_files/starfiles/tomo44_43s_eif4g_data.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/juliette/Desktop/40S_files/starfiles/tomo44_60s_data.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/juliette/Desktop/40S_files/starfiles/tomo44_80s_data.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list tomo44_40s_eif5b_data.star with 23 particles.  
Opened Particle list tomo44_40s_empty_data.star with 37 particles.  
Opened Particle list tomo44_43s_data.star with 46 particles.  
Opened Particle list tomo44_43s_eif4g_data.star with 20 particles.  
Opened Particle list tomo44_60s_data.star with 85 particles.  
Opened Particle list tomo44_80s_data.star with 557 particles.  

> open /Users/juliette/Desktop/maps_ans_finalM/4h_ans/decE_filtlocal.mrc

Opened decE_filtlocal.mrc as #2, grid size 184,184,184, pixel 4.34, shown at
level 0.00685, step 1, values float32  

> view

> volume #2 level 0.01594

> artiax particles #1.2.6 color 37,95,95,100

set axis size 65.1  
65.1  
['.arrow', '0', '0', '0', '65.1', '0', '0', '4.34', '17.36']  

> artiax particles #1.2.6 originScaleFactor 4.34

> artiax view xy

> artiax attach #2 toParticleList #1.2.6

Opened decE_filtlocal.mrc as #1.2.6.1.1, grid size 184,184,184, pixel 4.34,
shown at level 0.00685, step 1, values float32  

> volume #1.2.6.1.1 capFaces false

> open /Users/juliette/Desktop/40S_files/averages/4h_40s_eif5b.mrc

Opened 4h_40s_eif5b.mrc as #2, grid size 128,128,128, pixel 4.34, shown at
level 0.373, step 1, values float32  

> artiax particles #1.2.1 color 58,100,71,100

set axis size 65.1  
65.1  
['.arrow', '0', '0', '0', '65.1', '0', '0', '4.34', '17.36']  

> artiax particles #1.2.1 originScaleFactor 4.34

> artiax view xy

> view

> center #2

Unknown command: center #2  

> center #

Unknown command: center #  

> center #

Unknown command: center #  

> center #2

Unknown command: center #2  

> view #2

> volume #2 level 0.1885

> artiax attach #2 toParticleList #1.2.1

Opened 4h_40s_eif5b.mrc as #1.2.1.1.1, grid size 128,128,128, pixel 4.34,
shown at level 0.373, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> view

> artiax particles #1.2.2 color 0,46,86,100

> open /Users/juliette/Desktop/40S_files/averages/4h_40s_empty.mrc

Opened 4h_40s_empty.mrc as #2, grid size 128,128,128, pixel 4.34, shown at
level 0.383, step 1, values float32  

> view #3

No objects specified.  

> view #2

> volume #2 level 0.1476

> artiax attach #2 toParticleList #1.2.2

Opened 4h_40s_empty.mrc as #1.2.2.1.1, grid size 128,128,128, pixel 4.34,
shown at level 0.383, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> view

set axis size 65.1  
65.1  
['.arrow', '0', '0', '0', '65.1', '0', '0', '4.34', '17.36']  

> artiax particles #1.2.2 originScaleFactor 4.34

> artiax view xy

> artiax particles #1.2.3 color 94,64,100,100

> open /Users/juliette/Desktop/40S_files/averages/4h_43s.mrc

Opened 4h_43s.mrc as #2, grid size 128,128,128, pixel 4.34, shown at level
0.406, step 1, values float32  

> view #2

> volume #2 level 0.1377

> volume #2 level 0.1534

set axis size 65.1  
65.1  
['.arrow', '0', '0', '0', '65.1', '0', '0', '4.34', '17.36']  

> artiax particles #1.2.3 originScaleFactor 4.34

> artiax view xy

> artiax attach #2 toParticleList #1.2.3

Opened 4h_43s.mrc as #1.2.3.1.1, grid size 128,128,128, pixel 4.34, shown at
level 0.406, step 1, values float32  

> volume #1.2.3.1.1 capFaces false

> set bgColor white

> color #1.2.2 #3366ccff models

> color #1.2.2 #6699ffff models

> color #1.2.1 #99ffccff models

> color #1.2.1 #99cc99ff models

> color #1.2.3 #ff99ffff models

> color #1.2.3 #ff99ccff models

> color #1.2.6 #66ffffff models

> color #1.2.6 #99ffffff models

> color #1.2.6 #ccffffff models

> color #1.2.6 #ccffff4d models

> color #1.2.6 #ccffff80 models

> graphics silhouettes true

> graphics silhouettes width 1

> hide #!1.2.5 models

> hide #!1.2.4 models

> open /Users/juliette/Desktop/40S_files/segmentations/tomo44_seg_clean.mrc

Opened tomo44_seg_clean.mrc as #2, grid size 500,712,376, pixel
17.4,17.4,17.4, shown at level 0.011, step 2, values int16  

> select down

Nothing selected  

> volume #2 surfaceSmoothing true smoothingIterations 10

> volume #2 color white

> volume #1.2.6.1.1 level 0.01142

> artiax start

[Repeated 1 time(s)]

> hide #!1.2.6.1.1 models

> show #!1.2.6.1.1 models

> hide #1.2.6.1.1.1 models

> show #1.2.6.1.1.1 models

> volume #1.2.6.1.1 level 0.02866

> volume #1.2.6.1.1 level 0.01451

> save /Users/juliette/Desktop/40S_files/chimerax/tomo44_artiax.cxs
> includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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/juliette/Library/Application Support/ChimeraX/1.5/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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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' ->
<chimerax.core.attributes.RegAttrManager object at 0x107db4cd0> ->
<chimerax.atomic.molobject.Atom object at 0x1577b2a80> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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/juliette/Library/Application Support/ChimeraX/1.5/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-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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' ->
<chimerax.core.attributes.RegAttrManager object at 0x107db4cd0> ->
<chimerax.atomic.molobject.Atom object at 0x1577b2a80> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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.  
  

> view

> artiax start

[Repeated 1 time(s)]

> view

> view orient

> ui tool show "Side View"

> lighting gentle

> lighting depthCue true

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting soft

> color #1.2.6 #ccffffff models

> lighting gentle

> undo

Undo failed, probably because structures have been modified.  

> graphics silhouettes false

> view orient

> lighting simple

> view

> graphics silhouettes true

> lighting simple

> color #1.2.6 #ccffff80 models

> lighting soft

> save /Users/juliette/Desktop/40S_files/tomo44_artiax_1.png width 2100 height
> 1658 supersample 4

> open help:user/artiax_index.html

Opened help:user/artiax_index.html  

> options

Unknown command: artiax options  

> Options

Unknown command: artiax Options  

> stop

Unknown command: artiax stop  

> artiax show surfaces

> artiax hide surfaces

> artiax show surfaces

> artiax start

> artiax show markers

[Repeated 1 time(s)]

> artiax hide markers

[Repeated 2 time(s)]

> artiax hide axes

> view

[Repeated 1 time(s)]

> view orient

> ui tool show "Side View"

> view

> view orient

> ui mousemode right zoom

> save /Users/juliette/Desktop/40S_files/tomo44_artiax_2.png width 2100 height
> 1393 supersample 4

> save /Users/juliette/Desktop/40S_files/chimerax/tomo44_artiax.cxs
> includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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/juliette/Library/Application Support/ChimeraX/1.5/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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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' ->
<chimerax.core.attributes.RegAttrManager object at 0x107db4cd0> ->
<chimerax.atomic.molobject.Atom object at 0x1577b2a80> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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/juliette/Library/Application Support/ChimeraX/1.5/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-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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-1.5-rc2022.10.28.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' ->
<chimerax.core.attributes.RegAttrManager object at 0x107db4cd0> ->
<chimerax.atomic.molobject.Atom object at 0x1577b2a80> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Applications/ChimeraX-1.5-rc2022.10.28.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.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S001ZEN/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 14 jours, 3 heures et 17 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210282349
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.5
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.0
    starfile: 0.4.11
    superqt: 0.3.8
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0