Opened 19 months ago

Last modified 19 months ago

#14848 assigned defect

ArtiaX session save: Unknown class name 'MarkerSetPlus'

Reported by: rf2366@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.3.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Attempting to save a session while using ArtiaX with a tomogram, 3 particle lists and attached models, and a segmented membrane volume

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

  
Opened ay18112021_gridX_lamella2_pos5_15.68Apx.mrc as #1.1.1, grid size
512,512,256, pixel 15.7, shown at level 0.203, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> open /Users/rf2366/Downloads/ay18112021_gridX_lamella2_pos5_newriboind5.star
> format star

Summary of feedback from opening
/Users/rf2366/Downloads/ay18112021_gridX_lamella2_pos5_newriboind5.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list ay18112021_gridX_lamella2_pos5_newriboind5.star with 750
particles.  

> open /Users/rf2366/EZLab/subtomo2chimerax/ind5_good_particles/avg.mrc

Opened avg.mrc as #2, grid size 64,64,64, pixel 7.84, shown at level 0.0132,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened avg.mrc as #1.2.1.1.1, grid size 64,64,64, pixel 7.84, shown at level
0.0132, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

set axis size 58.5  
58.5  
['.arrow', '0', '0', '0', '58.5', '0', '0', '3.9', '15.6']  

> artiax particles #1.2.1 originScaleFactor 3.9

> artiax view xy

> artiax particles #1.2.1 transScaleFactor 3.9

> artiax view xy

> open /Users/rf2366/Downloads/ay18112021_gridX_lamella2_pos5_FAS.star format
> star

Summary of feedback from opening
/Users/rf2366/Downloads/ay18112021_gridX_lamella2_pos5_FAS.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list ay18112021_gridX_lamella2_pos5_FAS.star with 35
particles.  

> open /Users/rf2366/Downloads/ref167_lp_14.mrc

Opened ref167_lp_14.mrc as #2, grid size 300,300,300, pixel 1.96, shown at
level 0.504, step 2, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened ref167_lp_14.mrc as #1.2.2.1.1, grid size 300,300,300, pixel 1.96,
shown at level 0.504, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

set axis size 29.25  
29.25  
['.arrow', '0', '0', '0', '29.25', '0', '0', '1.95', '7.8']  

> artiax particles #1.2.2 originScaleFactor 1.95

> artiax view xy

> artiax particles #1.2.2 transScaleFactor 1.95

> artiax view xy

> open
> /Users/rf2366/Downloads/ay18112021_gridX_lamella2_pos5_ribo_membrane.star
> format star

Summary of feedback from opening
/Users/rf2366/Downloads/ay18112021_gridX_lamella2_pos5_ribo_membrane.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list ay18112021_gridX_lamella2_pos5_ribo_membrane.star with 9
particles.  

> open /Users/rf2366/EZLab/subtomo2chimerax/ind5_good_particles/avg.mrc

Opened avg.mrc as #2, grid size 64,64,64, pixel 7.84, shown at level 0.0132,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.3

Opened avg.mrc as #1.2.3.1.1, grid size 64,64,64, pixel 7.84, shown at level
0.0132, step 1, values float32  

> volume #1.2.3.1.1 capFaces false

set axis size 58.5  
58.5  
['.arrow', '0', '0', '0', '58.5', '0', '0', '3.9', '15.6']  

> artiax particles #1.2.3 originScaleFactor 3.9

> artiax view xy

> artiax particles #1.2.3 transScaleFactor 3.9

> artiax view xy

> artiax particles #1.2.3 surfaceLevel 0.00722

> artiax particles #1.2.2 surfaceLevel 0.35505

> artiax particles #1.2.2 surfaceLevel 0.43777

> artiax particles #1.2.1 surfaceLevel 0.00813

> artiax particles #1.2.1 color 94,64,100,100

> artiax particles #1.2.1 color 36,68,55,100

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

> artiax particles #1.2.2 color 31,60,80,100

> artiax particles #1.2.3 color 60,25,0,100

> artiax particles #1.2.3 color 98,68,100,100

> open
> /Users/rf2366/EZLab/FAS_figs/tomo1_seg_region_4755608_region_3258807_region_2964758.mrc

Opened tomo1_seg_region_4755608_region_3258807_region_2964758.mrc as #2, grid
size 806,806,294, pixel 10, shown at level 1, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.852

> set bgColor white

> close #1.2.3.1.1

> close #1.2.2.1.1

> close #1.2.1.1.1

> close #1.1.1

> close #2

Opened ay18112021_gridX_lamella1_pos2_15.68Apx.mrc as #1.1.1, grid size
512,512,256, pixel 15.7, shown at level 0.228, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> open
> /Users/rf2366/Downloads/ay18112021_gridX_lamella1_pos2_ribo_membrane.star
> format star

Summary of feedback from opening
/Users/rf2366/Downloads/ay18112021_gridX_lamella1_pos2_ribo_membrane.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list ay18112021_gridX_lamella1_pos2_ribo_membrane.star with 10
particles.  

> open /Users/rf2366/EZLab/subtomo2chimerax/ind5_good_particles/avg.mrc

Opened avg.mrc as #2, grid size 64,64,64, pixel 7.84, shown at level 0.0132,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened avg.mrc as #1.2.1.1.1, grid size 64,64,64, pixel 7.84, shown at level
0.0132, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

set axis size 58.5  
58.5  
['.arrow', '0', '0', '0', '58.5', '0', '0', '3.9', '15.6']  

> artiax particles #1.2.1 originScaleFactor 3.9

> artiax view xy

> artiax particles #1.2.1 transScaleFactor 3.9

> artiax view xy

> open /Users/rf2366/Downloads/ay18112021_gridX_lamella1_pos2_newriboind5.star
> format star

Summary of feedback from opening
/Users/rf2366/Downloads/ay18112021_gridX_lamella1_pos2_newriboind5.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list ay18112021_gridX_lamella1_pos2_newriboind5.star with 333
particles.  

> open /Users/rf2366/EZLab/subtomo2chimerax/ind5_good_particles/avg.mrc

Opened avg.mrc as #2, grid size 64,64,64, pixel 7.84, shown at level 0.0132,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened avg.mrc as #1.2.2.1.1, grid size 64,64,64, pixel 7.84, shown at level
0.0132, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

set axis size 58.5  
58.5  
['.arrow', '0', '0', '0', '58.5', '0', '0', '3.9', '15.6']  

> artiax particles #1.2.2 originScaleFactor 3.9

> artiax view xy

> artiax particles #1.2.2 transScaleFactor 3.9

> artiax view xy

> open /Users/rf2366/Downloads/ay18112021_gridX_lamella1_pos2_FAS.star format
> star

Summary of feedback from opening
/Users/rf2366/Downloads/ay18112021_gridX_lamella1_pos2_FAS.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list ay18112021_gridX_lamella1_pos2_FAS.star with 21
particles.  

> open /Users/rf2366/Downloads/ref167_lp_14.mrc

Opened ref167_lp_14.mrc as #2, grid size 300,300,300, pixel 1.96, shown at
level 0.504, step 2, values float32  

> artiax attach #2 toParticleList #1.2.3

Opened ref167_lp_14.mrc as #1.2.3.1.1, grid size 300,300,300, pixel 1.96,
shown at level 0.504, step 1, values float32  

> volume #1.2.3.1.1 capFaces false

set axis size 29.25  
29.25  
['.arrow', '0', '0', '0', '29.25', '0', '0', '1.95', '7.8']  

> artiax particles #1.2.3 originScaleFactor 1.95

> artiax view xy

> artiax particles #1.2.3 transScaleFactor 1.95

> artiax view xy

> artiax particles #1.2.3 radius 0.1

set axis size 19.20809  
19.20809  
['.arrow', '0', '0', '0', '19.20809', '0', '0', '1.2805393333333333',
'5.122157333333333']  
set axis size 17.73824  
17.73824  
['.arrow', '0', '0', '0', '17.73824', '0', '0', '1.1825493333333335',
'4.730197333333334']  
set axis size 14.79853  
14.79853  
['.arrow', '0', '0', '0', '14.79853', '0', '0', '0.9865686666666666',
'3.9462746666666666']  
set axis size 8.91912  
8.91912  
['.arrow', '0', '0', '0', '8.91912', '0', '0', '0.5946079999999999',
'2.3784319999999997']  
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 #1.2.3 axesSize 0.1

> artiax particles #1.2.2 radius 0.1

set axis size 55.21949  
55.21949  
['.arrow', '0', '0', '0', '55.21949', '0', '0', '3.6812993333333335',
'14.725197333333334']  
set axis size 54.48456  
54.48456  
['.arrow', '0', '0', '0', '54.48456', '0', '0', '3.632304', '14.529216']  
set axis size 53.01471  
53.01471  
['.arrow', '0', '0', '0', '53.01471', '0', '0', '3.534314', '14.137256']  
set axis size 50.075  
50.075  
['.arrow', '0', '0', '0', '50.075', '0', '0', '3.3383333333333334',
'13.353333333333333']  
set axis size 44.93051  
44.93051  
['.arrow', '0', '0', '0', '44.93051', '0', '0', '2.9953673333333333',
'11.981469333333333']  
set axis size 36.1114  
36.1114  
['.arrow', '0', '0', '0', '36.1114', '0', '0', '2.407426666666667',
'9.629706666666667']  
set axis size 24.35257  
24.35257  
['.arrow', '0', '0', '0', '24.35257', '0', '0', '1.6235046666666666',
'6.494018666666666']  
set axis size 17.73824  
17.73824  
['.arrow', '0', '0', '0', '17.73824', '0', '0', '1.1825493333333335',
'4.730197333333334']  
set axis size 8.18419  
8.18419  
['.arrow', '0', '0', '0', '8.18419', '0', '0', '0.5456126666666666',
'2.1824506666666665']  
set axis size 1.56985  
1.56985  
['.arrow', '0', '0', '0', '1.56985', '0', '0', '0.10465666666666666',
'0.41862666666666665']  
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

> artiax particles #1.2.1 radius 0.1

set axis size 61.83382  
61.83382  
['.arrow', '0', '0', '0', '61.83382', '0', '0', '4.122254666666667',
'16.489018666666666']  
set axis size 61.0989  
61.0989  
['.arrow', '0', '0', '0', '61.0989', '0', '0', '4.07326', '16.29304']  
set axis size 59.62904  
59.62904  
['.arrow', '0', '0', '0', '59.62904', '0', '0', '3.9752693333333338',
'15.901077333333335']  
set axis size 50.075  
50.075  
['.arrow', '0', '0', '0', '50.075', '0', '0', '3.3383333333333334',
'13.353333333333333']  
set axis size 36.84632  
36.84632  
['.arrow', '0', '0', '0', '36.84632', '0', '0', '2.456421333333333',
'9.825685333333332']  
set axis size 17.00331  
17.00331  
['.arrow', '0', '0', '0', '17.00331', '0', '0', '1.133554', '4.534216']  
set axis size 5.24449  
5.24449  
['.arrow', '0', '0', '0', '5.24449', '0', '0', '0.34963266666666665',
'1.3985306666666666']  
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 surfaceLevel 0.00772

> artiax particles #1.2.2 surfaceLevel 0.01134

> artiax particles #1.2.3 surfaceLevel 0.34532

> artiax particles #1.2.3 color 60,25,0,100

> artiax particles #1.2.3 color 31,60,80,100

> artiax particles #1.2.3 color 66,69,96,100

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

> artiax particles #1.2.2 color 98,68,100,100

> artiax particles #1.2.2 color 36,68,55,100

> artiax particles #1.2.1 color 94,64,100,100

> artiax particles #1.2.1 color 98,68,100,100

> open
> /Users/rf2366/EZLab/FAS_figs/tomo1_seg_region_4755608_region_3258807_region_2964758.mrc

Opened tomo1_seg_region_4755608_region_3258807_region_2964758.mrc as #2, grid
size 806,806,294, pixel 10, shown at level 1, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.7075

> close #2

> open /Users/rf2366/EZLab/FAS_figs/segtest.mrc

Opened segtest.mrc as #2, grid size 802,802,402, pixel 10, shown at level 62,
step 4, values float32  

> volume #2 step 1

> volume #2 level 55.88

> ui tool show "Hide Dust"

> surface dust #2 size 20.8

> surface dust #2 size 20.15

> surface dust #2 size 948.42

> surface dust #2 size 1060

> surface dust #2 size 1793.1

> turn y 180

> turn x 90

> turn x -90

> turn z -90

> clip model #2 true

> volume #2 color #4f9acc

> ui tool show "Side View"

> artiax tomo #1.1.1 slice 200

> surface dust #2 size 1735.8

> surface dust #2 size 2627.2

> artiax tomo #1.1.1 slice 151

> lighting soft

> save /Users/rf2366/EZLab/FAS_figs/tomo2_v4.png width 1400 height 1851
> supersample 3

> lighting simple

> save /Users/rf2366/EZLab/FAS_figs/tomo__2.cxs

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "/Users/rf2366/Library/Application Support/ChimeraX/1.7/lib/python/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
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 0x11007a0d0> ->
<chimerax.atomic.molobject.Atom object at 0x15df51950> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "/Users/rf2366/Library/Application Support/ChimeraX/1.7/lib/python/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
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 0x11007a0d0> ->
<chimerax.atomic.molobject.Atom object at 0x15df51950> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.7.1/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: 4.1 Metal - 88
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_US.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: Mac
      Model Identifier: Mac14,9
      Model Number: Z17G002JCLL/A
      Chip: Unknown
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3.1 (23D60)
      Kernel Version: Darwin 23.3.0
      Time since boot: 9 days, 14 hours, 47 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    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: 2022.12.7
    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: 0.3
    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
    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: 21.3
    pandas: 2.2.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    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
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 15.0.2
    pycollada: 0.7.2
    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
    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
    setuptools-scm: 7.0.5
    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
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    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

Change History (4)

comment:1 by Eric Pettersen, 19 months ago

Cc: Eric Pettersen added
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, 19 months ago

Hi Ryan,

This is indeed a problem in ArtiaX, which has been reported a few times since the ArtiaX 0.3 release, but no fix yet. Do you know how to program Python? If you do, I could guide you in modifying the ArtiaX code in a way that I *think* will fix the problem (I'm not an ArtiaX programmer).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Utz Ermel, 19 months ago 

Hi Eric and Ryan, 

Saving in ChimeraX sessions is now supported starting with ArtiaX version 0.4.1, which I have just released on the toolshed (available for  ChimeraX 1.7.1). Also available here: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FrangakisLab_ArtiaX_releases_tag_0.4&d=DwIFaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=CKzZmwKi9_YVvHng-0ezdJFE-0MROfpdFWLsI4CZgtQ&m=Hc18sX-DfMoPaIdOava_34pNP2IipOZW1TiRbELF0qr92jQi1bcUzTvWl6MffRhy&s=8Uwy0GoIxkxHqUQTnvn5g2IFs89K1TyhYYhF2kwKSqQ&e=

Best, 
Utz

comment:4 by rf2366@…, 19 months ago 

Hi,

Eric and Utz,

I\u2019m sorry I missed your first message, I would have been up for the challenge. I\u2019m glad to hear Utz provided a fix though as I\u2019m sure it would have taken me much longer. Thank you both, ArtiaX is great!

Best regards,

Ryan

>
>
>
>
>> On 1. Apr 2024, at 10:20, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
>>
>> #14848: ArtiaX session save: Unknown class name 'MarkerSetPlus'
>> ----------------------------------+-----------------------
>>         Reporter:  rf2366@\u2026     |      Owner:  Utz Ermel
>>             Type:  defect       |     Status:  assigned
>>         Priority:  normal       |  Milestone:
>>        Component:  Third Party  |    Version:
>>       Resolution:               |   Keywords:
>>       Blocked By:               |   Blocking:
>> Notify when closed:               |   Platform:  all
>>          Project:  ChimeraX     |
>> ----------------------------------+-----------------------
>> Comment (by pett):
>>
>> Hi Ryan,
>>        This is indeed a problem in ArtiaX, which has been reported a few
>> times since the ArtiaX 0.3 release, but no fix yet. Do you know how to
>> program Python? If you do, I could guide you in modifying the ArtiaX code
>> in a way that I *think* will fix the problem (I'm not an ArtiaX
>> programmer).
>>
>> --Eric
>>
>>        Eric Pettersen
>>        UCSF Computer Graphics Lab
>> --
>> Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14848#comment:2>
>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
>> ChimeraX Issue Tracker
>
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