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Opened 3 years ago
Last modified 3 years ago
#7569 assigned defect
Session save: Unknown class name 'MarkerSetPlus'
| Reported by: | 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
(Describe the actions that caused this problem to occur here)
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 46Mi 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 (1)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session save: Unknown class name 'MarkerSetPlus' |
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