Opened 3 years ago

Last modified 19 months ago

#7570 assigned defect

Session save: Unknown class name 'MarkerSetPlus'

Reported by: liv.zimmermann@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.18.0-408.el8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I am not able to save the output file including a 3D volume and cropped particles I positioned using the ArtiaX package.

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /net/urz/sds-
> hd/sd18g002/Liv/DMVs/Manuscript/Figure1/Amira/final_surf.obj.gz

Opened OBJ file final_surf.obj.gz containing 1 objects, 12278890 triangles  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

> ui mousemode right select

> ui mousemode right "mark surface"

> ui mousemode right select

> hide #1 models

> show #1 models

> open /net/urz/sds-
> hd/sd18g002/Xiaohan/Krios/STA/20220409_wt/TS_03_dipole_artiax.Data/crop.tbl

Summary of feedback from opening /net/urz/sds-
hd/sd18g002/Xiaohan/Krios/STA/20220409_wt/TS_03_dipole_artiax.Data/crop.tbl  
---  
notes | Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black  
    lighting depthCue false  
    camera ortho

  
  
  
Opened Particle list crop.tbl with 117 particles.  

> open /net/urz/sds-
> hd/sd18g002/Xiaohan/Krios/STA/20220409_wt/wt_average_293_C6_template02/results/ite_0006/averages/average_symmetrized_ref_001_ite_0006_filteredflipzcopy.mrc

Opened average_symmetrized_ref_001_ite_0006_filteredflipzcopy.mrc as #3, grid
size 256,256,256, pixel 2.16, shown at level 2.07, step 1, values float32  

> volume scale #3 factor -1

Opened average_symmetrized_ref_001_ite_0006_filteredflipzcopy.mrc scaled as
#4, grid size 256,256,256, pixel 2.16, shown at step 1, values float32  

> volume #4 level 1.201

> volume #4 level 0.08947

> volume #4 level 0.341

> surface dust #4 size 50

> surface dust #4 size 60

> surface dust #4 size 70

> surface dust #4 size 75

> surface dust #4 size 80

> artiax attach #4 toParticleList #2.2.1

Opened average_symmetrized_ref_001_ite_0006_filteredflipzcopy.mrc scaled as
#2.2.1.1.1, grid size 256,256,256, pixel 2.16, shown at level 2.46, step 1,
values float32  

> volume #2.2.1.1.1 capFaces false

> artiax hide axes

> volume #2.2.1.1.1 level 0.6983

> artiax particles #2.2.1 surfaceLevel -2.10458

> artiax particles #2.2.1 surfaceLevel 0.39643

> artiax particles #2.2.1 color 58,100,71,100

> artiax particles #2.2.1 surfaceLevel 0.16196

> artiax particles #2.2.1 surfaceLevel 0.42248

> artiax particles #2.2.1 surfaceLevel 0.60485

> artiax particles #2.2.1 surfaceLevel 1.07379

> artiax particles #2.2.1 originScaleFactor 2.0

> artiax view xy

> artiax particles #2.2.1 originScaleFactor 3.0

> artiax view xy

> ui mousemode right rotate

> ui mousemode right "rotate selected particles"

[Repeated 1 time(s)]

> ui mousemode right select

Drag select of final_surf.obj.gz, 1356 of 12278890 triangles, surfaces, 2 of
117 instances, 2 atoms  

> select clear

Drag select of final_surf.obj.gz, 58450 of 12278890 triangles, surfaces, 2 of
117 instances, 2 atoms  
Drag select of final_surf.obj.gz, 364 of 12278890 triangles, surfaces, 1 of
117 instances, 1 atoms  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.71419,-0.14301,-0.68519,3003.9,-0.62569,0.30838,-0.71653,8482.6,0.31377,0.94045,0.13076,-7232.8,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.7843,-0.61592,-0.074256,5413.8,0.62034,0.77718,0.10566,-80.129,-0.0073691,-0.12893,0.99163,426.56,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.74554,-0.23291,0.62443,3756.3,0.27863,0.96006,0.025429,1219,-0.60541,0.15503,0.78067,2871.1,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.95833,-0.073715,0.27599,12401,-0.21088,0.83429,-0.50941,4094.1,-0.1927,-0.54638,-0.81507,2445.6,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.89921,-0.023551,-0.43689,771.48,0.16436,0.9436,0.28742,1623.2,0.40548,-0.33026,0.85236,-1563.1,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.92204,0.032728,-0.3857,364.42,0.073787,0.96329,0.25813,2096.4,0.37999,-0.26647,0.88578,-1701.4,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.36179,0.55428,0.74959,5756.2,-0.48237,0.57675,-0.6593,7470.7,-0.79777,-0.6001,0.058707,7273.8,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.85473,0.30635,-0.41904,-419.19,0.051909,0.75277,0.65623,3184,0.51648,-0.58265,0.62751,-972.98,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.87647,0.2161,-0.43023,10862,0.42223,0.77439,-0.47122,1387.2,0.23134,-0.59466,-0.76997,1646.4,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.70197,0.69336,-0.16279,-1279.5,-0.35271,0.53701,0.7663,7289.8,0.61874,-0.4805,0.62152,-1390.7,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.61111,-0.69208,0.38416,5540.6,-0.28139,0.26368,0.92266,8078.7,-0.73984,-0.67194,-0.033607,7946.2,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,0.24135,-0.95291,0.18361,9159.7,-0.95296,-0.19697,0.23038,15009,-0.18337,-0.23058,-0.95562,3837.8,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.083078,0.74499,0.66188,3735,-0.99347,-0.11405,0.0036717,14896,0.078223,-0.65726,0.7496,4066.9,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.20931,0.97633,0.054546,3414.6,-0.9769,-0.21124,0.03233,15211,0.043087,-0.046519,0.99799,1744.7,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.20537,0.87091,-0.44648,3777.6,-0.9589,-0.27032,-0.086231,15343,-0.19579,0.41042,0.89063,1178,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.21659,0.96676,-0.13588,3426.9,-0.96201,-0.23505,-0.13887,15206,-0.1662,0.10064,0.98094,2359.9,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.21659,0.96676,-0.13588,2806.5,-0.96201,-0.23505,-0.13887,15253,-0.1662,0.10064,0.98094,2261.3,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.21659,0.96676,-0.13588,1209.8,-0.96201,-0.23505,-0.13887,16254,-0.1662,0.10064,0.98094,2106,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models
> #1,-0.21659,0.96676,-0.13588,1409.2,-0.96201,-0.23505,-0.13887,15934,-0.1662,0.10064,0.98094,2103.6,#2.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1.3,1,0,0,0,0,1,0,0,0,0,1,0

117 atoms, 117 residues, atom tag range 1 to 117  
[Repeated 1 time(s)]

> artiax colormap #2.2.1.3 tag palette redgreen minValue 1.0 maxValue 117.0
> transparency 0.0

117 atoms, 117 residues, atom tag range 1 to 117  
[Repeated 1 time(s)]

> artiax colormap #2.2.1.3 tag palette redgreen minValue 1.0 maxValue 117.0
> transparency 0.0

> artiax particles #2.2.1 color 58,100,71,100

> ui mousemode right select

> save /net/urz/sds-
> hd/sd18g002/Liv/DMVs/Manuscript/Figure1/ChimeraX/model_TS03.cxs

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/home/bq_lizimmermann/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/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 0x7f52f3af0550> ->
<chimerax.atomic.molobject.Atom object at 0x7f5243e3c080> 'M': Unknown class
name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/home/bq_lizimmermann/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/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 0x7f52f3af0550> ->
<chimerax.atomic.molobject.Atom object at 0x7f5243e3c080> 'M': Unknown class
name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "/usr/libexec/UCSF-ChimeraX/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.  
  

> cd /net/urz/sds-hd/sd18g002/Liv/DMVs/Manuscript/Figure1/ChimeraX

Current working directory is: /net/urz/sds-
hd/sd18g002/Liv/DMVs/Manuscript/Figure1/ChimeraX  
No map chosen to save  
[Repeated 1 time(s)]Drag select of final_surf.obj.gz, 5704 of 12278890
triangles  

> select clear

[Repeated 2 time(s)]Drag select of final_surf.obj.gz, 150431 of 12278890
triangles  
Drag select of final_surf.obj.gz, 68299 of 12278890 triangles  

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.21659,0.96676,-0.13588,-855.41,-0.96201,-0.23505,-0.13887,16260,-0.1662,0.10064,0.98094,1716.2

> view matrix models
> #1,-0.21659,0.96676,-0.13588,3682.2,-0.96201,-0.23505,-0.13887,17302,-0.1662,0.10064,0.98094,2475

> view matrix models
> #1,-0.21659,0.96676,-0.13588,1371.8,-0.96201,-0.23505,-0.13887,15794,-0.1662,0.10064,0.98094,2098.6

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.29362,0.94439,-0.14805,1948.2,-0.93892,-0.314,-0.14084,15998,-0.1795,0.097656,0.9789,2194.3

> view matrix models
> #1,0.92769,0.37302,-0.015788,-3111.1,-0.37271,0.92775,0.019234,7013.8,0.021822,-0.011959,0.99969,1428.3

> view matrix models
> #1,-0.54279,0.26889,-0.79566,6466.9,-0.021426,0.94262,0.33317,4770.6,0.8396,0.19789,-0.50588,-4580.4

> view matrix models
> #1,-0.97494,0.19247,0.11155,9491.1,0.1965,0.98015,0.026239,3251,-0.10429,0.047502,-0.99341,1935.9

> view matrix models
> #1,-0.9697,0.092601,0.22605,9899.4,0.20052,0.83024,0.52008,3889.9,-0.13952,0.54966,-0.82366,-57.308

> view matrix models
> #1,-0.95552,-0.26795,0.12324,11400,0.20853,-0.31829,0.92478,8904.2,-0.20857,0.90934,0.36,-1206.3

> view matrix models
> #1,-0.90639,-0.37068,-0.20263,11545,0.29931,-0.90198,0.31121,10909,-0.29812,0.22143,0.92849,2384.6

> view matrix models
> #1,-0.95139,-0.30147,-0.062999,11521,0.30521,-0.95026,-0.062009,11083,-0.041171,-0.078223,0.99609,2111.2

> ui mousemode right select

[Repeated 1 time(s)]

> hide #!2.2.1 models

> show #!2.2.1 models

> cd /net/urz/sds-hd/sd18g002/Liv/DMVs/Manuscript/Figure1/ChimeraX

Current working directory is: /net/urz/sds-
hd/sd18g002/Liv/DMVs/Manuscript/Figure1/ChimeraX  

> save /net/urz/sds-hd/sd18g002/Liv/DMVs/Manuscript/Figure1/ChimeraX/TS03.cxs
> includeMaps true

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/home/bq_lizimmermann/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/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 0x7f52f3af0550> ->
<chimerax.atomic.molobject.Atom object at 0x7f5243e3c080> 'M': Unknown class
name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/home/bq_lizimmermann/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/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 0x7f52f3af0550> ->
<chimerax.atomic.molobject.Atom object at 0x7f5243e3c080> 'M': Unknown class
name 'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File "/usr/libexec/UCSF-ChimeraX/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: 3.3.0 NVIDIA 515.65.01
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: X299 UD4
OS: CentOS Stream 8 
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Core(TM) i9-7960X CPU @ 2.80GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       4.5Gi        35Gi        42Mi        22Gi        57Gi
	Swap:          31Gi       363Mi        31Gi

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:85f1]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    pandas: 1.4.4
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    starfile: 0.4.11
    suds-community: 1.0.0
    superqt: 0.3.5
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.3.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

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

comment:2 by Utz Ermel, 19 months ago 

Dear Liv,

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). It is also available on the ArtiaX GitHub repository. 

To install the new version using the toolshed run the following commands in ChimeraX 1.7.1:

toolshed reload available
toolshed install ArtiaX

Best, 
Utz
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