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#18772 closed defect (duplicate)

ArtiaX session save: 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-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/denoised.transformed.mrc

Summary of feedback from opening
D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/denoised.transformed.mrc  
---  
note | D:\课题\LPOR写文章\AI作图\2_1_BigFilament在原位结构作图\7136\0910\denoised.transformed.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened denoised.transformed.mrc as #1, grid size 1024,1440,210, pixel 1, shown
at step 1, values uint8  

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/cellmembrane_fromAmira/denoised.masked.mrc

Summary of feedback from opening
D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/cellmembrane_fromAmira/denoised.masked.mrc  
---  
note | D:\课题\LPOR写文章\AI作图\2_1_BigFilament在原位结构作图\7136\0910\cellmembrane_fromAmira\denoised.masked.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened denoised.masked.mrc as #2, grid size 1024,1440,210, pixel 1, shown at
step 1, values uint8  

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/cellmembrane_fromEMAN/denoised.transformed__good_1_seg.hdf

Opened denoised.transformed__good_1_seg.hdf as #3, grid size 1024,1440,216,
pixel 1, shown at step 1, values float32  

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/Filament_from_Amira/denoised_2_dilated.view.mrc
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/Filament_from_Amira/denoised_3_dilated.view.mrc

Summary of feedback from opening files  
---  
notes | D:\课题\LPOR写文章\AI作图\2_1_BigFilament在原位结构作图\7136\0910\Filament_from_Amira\denoised_2_dilated.view.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
D:\课题\LPOR写文章\AI作图\2_1_BigFilament在原位结构作图\7136\0910\Filament_from_Amira\denoised_3_dilated.view.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened denoised_2_dilated.view.mrc as #4.1, grid size 1024,1441,211, pixel 1,
shown at step 1, values uint8  
Opened denoised_3_dilated.view.mrc as #4.2, grid size 1024,1441,211, pixel 1,
shown at step 1, values uint8  

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/Protothylakoid_Membrane_fromAmira/denoised.masked.mrc

Summary of feedback from opening
D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/Protothylakoid_Membrane_fromAmira/denoised.masked.mrc  
---  
note | D:\课题\LPOR写文章\AI作图\2_1_BigFilament在原位结构作图\7136\0910\Protothylakoid_Membrane_fromAmira\denoised.masked.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened denoised.masked.mrc as #5, grid size 1024,1440,210, pixel 1, shown at
step 1, values uint8  

> close #5

> volume #2 region 0,0,0,1023,1439,209 step 4

[Repeated 1 time(s)]

> volume #2 level 80

> volume #2 change image level 0,0 level 127,0.8 level 213,1

> volume #3 region 0,0,0,1023,1439,215 step 4

[Repeated 1 time(s)]

> volume #2 step 1

> volume #3 step 1

> set bgColor white

> volume #4.1 region 0,0,0,1023,1440,210 step 4

[Repeated 1 time(s)]

> volume #4.2 region 0,0,0,1023,1440,210 step 4

[Repeated 1 time(s)]

> volume #4.1 step 1

> volume #4.2 step 1

> artiax start

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

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> set bgColor white

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/rubisco/rubisco_merge_other_7.coords
> format coords

Opened Particle list rubisco_merge_other_7.coords with 56353 particles.  

> artiax particles #5.2.1 axesSize 0.1

> artiax particles #5.2.1 radius 0.1

> artiax particles #5.2.1 axesSize 0.1

> artiax particles #5.2.1 radius 0.1

> artiax particles #5.2.1 axesSize 0.1

> artiax particles #5.2.1 radius 0.1

> artiax particles #5.2.1 axesSize 0.1

> open
> D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/7136/0910/rubisco/cryosparc_P19_J153_005_volume_map_sharp_lowpass20_102A.mrc

Opened cryosparc_P19_J153_005_volume_map_sharp_lowpass20_102A.mrc as #6, grid
size 30,30,30, pixel 1, shown at level 0.062, step 1, values float32  

> artiax attach #6 toParticleList #5.2.1

Opened cryosparc_P19_J153_005_volume_map_sharp_lowpass20_102A.mrc as
#5.2.1.1.1, grid size 30,30,30, pixel 1, shown at level 0.062, step 1, values
float32  

> volume #5.2.1.1.1 capFaces false

> artiax show #5.2.1 surfaces

> artiax particles #5.2.1 surfaceLevel 0.05922

> artiax particles #5.2.1 color 0,60,56,100

[Repeated 1 time(s)]

> artiax particles #5.2.1 color 13,60,44,100

> artiax particles #5.2.1 color 23,60,43,100

> artiax particles #5.2.1 color 24,60,58,100

> artiax particles #5.2.1 color 13,60,60,100

> artiax particles #5.2.1 color 6,60,44,100

> artiax particles #5.2.1 color 17,60,35,100

> artiax particles #5.2.1 color 9,60,43,100

> artiax particles #5.2.1 color 11,60,56,100

> artiax particles #5.2.1 color 8,60,41,100

> artiax particles #5.2.1 color 16,60,47,100

> save D:/1.cxs includeMaps true

Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000001CE8200F210> ->
<chimerax.atomic.molobject.Atom object at 0x000001CF90420710> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x000001CE8200F210> ->
<chimerax.atomic.molobject.Atom object at 0x000001CF90420710> 'M': Unknown
class name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> volume #3 color #7cfffb

> volume #3 color #87ffed

> volume #3 color #26ff34

> volume #3 color #6aff50

> volume #3 color #d8ff6b

> volume #3 color #f2ff7d

> volume #3 color #daff23

> volume #3 color #f0ff47

> volume #3 color #e5ff61

> volume #3 color #e7ff7e

> volume #3 color #ebff90

> volume #3 color #eeffbe

> volume #2 color #47ffff

> volume #2 color #21ffde

> volume #2 color #34ff93

> volume #4.1 color #de20ff

> volume #4.1 color #ff2277

> volume #4.1 color #ff348c

> volume #4.2 color #e6b2ff

> volume #4.2 color #e644ff

> volume #4.2 color #e6441d

> volume #2 color #ff37f5

> volume #2 color #dca0ff

> volume #2 color #ff83bf

> volume #2 color #3783bf

> volume #2 color #4a83bf

> volume #2 color #4a98bf

> volume #2 color #4a98de

> volume #2 color #f098de

> volume #2 color #f04fde

> volume #2 color #f04f04

> volume #2 color #014f04

> volume #2 color #d64f04

> volume #2 color #d68f04

> volume #2 color #d68fd7

> artiax particles #5.2.1 color 16,60,47,100

> artiax particles #5.2.1 color 0,60,47,100

> artiax particles #5.2.1 color 7,60,47,100

> artiax particles #5.2.1 color 72,60,47,100

> artiax particles #5.2.1 color 72,0,47,100

> artiax particles #5.2.1 color 72,7,47,100

> artiax particles #5.2.1 color 72,72,47,100

> artiax particles #5.2.1 color 72,72,0,100

> artiax particles #5.2.1 color 72,72,7,100

> artiax particles #5.2.1 color 72,72,72,100

> lighting soft

> volume #2 color #ff8fd7

> volume #2 color #ff08d7

> volume #2 color #ff5cd7

> volume #2 color #ff5cd6

> volume #2 color #ff5c00

> volume #4.1 color #61348c

> volume #4.1 color #61be8c

> volume #4.1 color #61beff

> volume #3 color #ebffbe

> volume #3 color #ebacbe

> volume #3 color #ebacbc

> volume #3 color #ebace9

> volume #3 color #eb31db

> volume #3 color #eb1245

> volume #3 color #eb16eb

> volume #3 color #bfebce

> volume #3 color #ebceb9

> volume #3 color #76675d

> volume #3 color #ab9687

> volume #3 color #c5ad9b

> volume #3 color #48c5b0

> volume #3 color #c5c575

> volume #3 color #c5c585

> volume #3 color #c5a49a

> volume #3 color #c5bdb1

> volume #2 color #d91cff

> volume #2 color #ff52df

> volume #2 color #e7aeff

> volume #2 color #e897ff

> volume #2 color #e0afff

> volume #4.2 color #e6cfa1

> volume #4.2 color #69dce6

> volume #4.2 color #21a1e6

> volume #4.2 color #e629d3

> volume #4.2 color #e688e1

> volume #4.2 color #1de681

> volume #4.2 color #61e60e

> volume #4.2 color #e6d5a9

> volume #4.2 color #5de674

> volume #4.2 color #19e60e

> volume #4.2 color #0be619

> volume #4.2 color #19e68a

> volume #4.2 color #0be6c5

> volume #4.1 color #ff55d2

> volume #4.1 color #ff26db

> volume #4.1 color #ff0c6d

> volume #4.1 color #ff218c

> volume #4.1 color #ff0856

> volume #4.1 color #ff2f89

> volume #4.1 color #ff113d

> volume #4.1 color #ff3e61

> volume #4.1 color #ff3485

> volume #4.1 color #ff0f4f

> volume #4.1 color #ff4b0f

> volume #4.1 color #ff4f30

> volume #4.1 color #ff8011

> volume #4.1 color #1a4cff

> volume #4.1 color #10c7ff

> volume #4.1 color #10ffb7

> volume #4.1 color #3967ff

> volume #4.1 color #ff0e4e

> volume #4.1 color blue

> volume #4.1 color #0055ff

> volume #4.1 color #ff17ec

> volume #4.1 color #ff0e46

> volume #4.1 color #ff2a4a

> volume #4.1 color #ff1c27

> volume #4.1 color #ff1768

> volume #4.1 color #ff2a8a

> volume #4.1 color #ff3884

> artiax particles #5.2.1 color 72,72,72,100

> artiax view xy

> artiax view xz

[Repeated 1 time(s)]

> artiax view yz

[Repeated 1 time(s)]

> artiax view xy

[Repeated 2 time(s)]

> save D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/20250912_7136.cxs includeMaps
> true

Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001CEFF3FE410>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001CEFF3FE410>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> save D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/20250912.cxs includeMaps true

Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001CEFF3FE410>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001CEFF3FE410>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> save D:/课题/LPOR写文章/AI作图/2_1_BigFilament在原位结构作图/20250912.cxs includeMaps true

Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001CEFF3FE410>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj  
uid = self.unique_name.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 175, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "C:\Users\jma\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\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 "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001CEFF3FE410>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File "D:\Program Files (x86)\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 3670
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 25,587,761,152
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    pandas: 2.2.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 20.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    starfile: 0.5.12
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 months ago

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

comment:2 by Eric Pettersen, 2 months ago

Resolution:	→ duplicate
Status:	assigned → closed

Fixed as of ArtiaX 0.4.1 (this ticket has 0.1)

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