Opened 3 years ago
Last modified 3 years ago
#8274 assigned defect
ArtiaX session save: Unknown class name 'MarkerSetPlus'
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-56-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Saving an artiaX session with cxs format.
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened 022_Lam18ts2_seg.mrc as #1.1.1, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0011, step 1, values int16
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
Opened 021_Lam18ts2_seg.mrc as #1.1.2, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00105, step 1, values int16
> artiax tomo #1.1.2 sliceDirection 0,0,1
> artiax view xy
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.2 models
> hide #!1.1.1 models
> show #!1.1.2 models
> show #!1.1.1 models
> volume #1.1.2 style surface
> volume #1.1.1 style surface
Opened 020_Lam18ts2_seg.mrc as #1.1.3, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.001, step 1, values int16
> artiax tomo #1.1.3 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.3 style mesh
> volume #1.1.3 style surface
Opened 019_Lam18ts2_seg.mrc as #1.1.4, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00095, step 1, values int16
> artiax tomo #1.1.4 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.4 style surface
Opened 018_Lam18ts2_seg.mrc as #1.1.5, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0009, step 1, values int16
> artiax tomo #1.1.5 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.5 style surface
Opened 017_Lam18ts2_seg.mrc as #1.1.6, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00085, step 1, values int16
> artiax tomo #1.1.6 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.6 style surface
Opened 016_Lam18ts2_seg.mrc as #1.1.7, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0008, step 1, values int16
> artiax tomo #1.1.7 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.7 style surface
Opened 015_Lam18ts2_seg.mrc as #1.1.8, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00075, step 1, values int16
> artiax tomo #1.1.8 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.8 style surface
> hide #!1.1.8 models
> show #!1.1.8 models
Opened 014_Lam18ts2_seg.mrc as #1.1.9, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0007, step 1, values int16
> artiax tomo #1.1.9 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.9 style surface
> hide #!1.1.9 models
> show #!1.1.9 models
Opened 013_Lam18ts2_seg.mrc as #1.1.10, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00065, step 1, values int16
> artiax tomo #1.1.10 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.10 style surface
> hide #!1.1.10 models
> show #!1.1.10 models
> hide #!1.1.10 models
> show #!1.1.10 models
Opened 012_Lam18ts2_seg.mrc as #1.1.11, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0006, step 1, values int16
> artiax tomo #1.1.11 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.11 style surface
> hide #!1.1.11 models
> show #!1.1.11 models
> hide #!1.1.11 models
> show #!1.1.11 models
Opened 011_Lam18ts2_seg.mrc as #1.1.12, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00055, step 1, values int16
> artiax tomo #1.1.12 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.12 style surface
> hide #!1.1.12 models
> show #!1.1.12 models
Opened 010_Lam18ts2_seg.mrc as #1.1.13, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0005, step 1, values int16
> artiax tomo #1.1.13 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.13 style surface
> hide #!1.1.13 models
> show #!1.1.13 models
Opened 009_Lam18ts2_seg.mrc as #1.1.14, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00045, step 1, values int16
> artiax tomo #1.1.14 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.14 style surface
> hide #!1.1.14 models
> show #!1.1.14 models
Opened 008_Lam18ts2_seg.mrc as #1.1.15, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0004, step 1, values int16
> artiax tomo #1.1.15 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.15 style surface
> hide #!1.1.15 models
> show #!1.1.15 models
Opened 007_Lam18ts2_seg.mrc as #1.1.16, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00035, step 1, values int16
> artiax tomo #1.1.16 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.15
> hide #!1.1.16 models
> show #!1.1.16 models
> hide #!1.1.16 models
> show #!1.1.16 models
> hide #!1.1.16 models
> show #!1.1.16 models
> volume #1.1.16 style surface
> hide #!1.1.16 models
> show #!1.1.16 models
> hide #!1.1.16 models
> show #!1.1.16 models
Opened 006_Lam18ts2_seg.mrc as #1.1.17, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0003, step 1, values int16
> artiax tomo #1.1.17 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.17 style surface
> hide #!1.1.17 models
> show #!1.1.17 models
Opened 005_Lam18ts2_seg.mrc as #1.1.18, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00025, step 1, values int16
> artiax tomo #1.1.18 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.18 style surface
> hide #!1.1.18 models
> show #!1.1.18 models
Opened 004_Lam18ts2_seg.mrc as #1.1.19, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0002, step 1, values int16
> artiax tomo #1.1.19 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.19 style surface
> hide #!1.1.19 models
> show #!1.1.19 models
Opened 003_Lam18ts2_seg.mrc as #1.1.20, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.00015, step 1, values int16
> artiax tomo #1.1.20 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.20 style surface
> hide #!1.1.20 models
> show #!1.1.20 models
Opened 002_Lam18ts2_seg.mrc as #1.1.21, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 0.0001, step 1, values int16
> artiax tomo #1.1.21 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.21 style surface
> hide #!1.1.21 models
> show #!1.1.21 models
Opened 001_Lam18ts2_seg.mrc as #1.1.22, grid size 510,720,188, pixel
16.6,16.6,16.6, shown at level 5e-05, step 1, values int16
> artiax tomo #1.1.22 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.22 style surface
> hide #!1.1.22 models
> show #!1.1.22 models
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class1.txt.txt.tbl
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class2.txt.txt.tbl
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class3.txt.txt.tbl
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class4.txt.txt.tbl
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_G2Class1.txt.txt.tbl
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_G2Class4.txt.txt.tbl
> format dynamo
Summary of feedback from opening
/media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class1.txt.txt.tbl
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Summary of feedback from opening
/media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class2.txt.txt.tbl
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Summary of feedback from opening
/media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class3.txt.txt.tbl
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Summary of feedback from opening
/media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_Class4.txt.txt.tbl
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Summary of feedback from opening
/media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_G2Class1.txt.txt.tbl
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Summary of feedback from opening
/media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_G2Class4.txt.txt.tbl
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list Lam18ts2_Class1.txt.txt.tbl with 31 particles.
Opened Particle list Lam18ts2_Class2.txt.txt.tbl with 10 particles.
Opened Particle list Lam18ts2_Class3.txt.txt.tbl with 7 particles.
Opened Particle list Lam18ts2_Class4.txt.txt.tbl with 2 particles.
Opened Particle list Lam18ts2_G2Class1.txt.txt.tbl with 3 particles.
Opened Particle list Lam18ts2_G2Class4.txt.txt.tbl with 2 particles.
set axis size 248.39999999999998
248.39999999999998
['.arrow', '0', '0', '0', '248.39999999999998', '0', '0', '16.56', '66.24']
> artiax particles #1.2.1 originScaleFactor 16.56
> artiax view xy
set axis size 248.39999999999998
248.39999999999998
['.arrow', '0', '0', '0', '248.39999999999998', '0', '0', '16.56', '66.24']
> artiax particles #1.2.2 originScaleFactor 16.56
> artiax view xy
set axis size 248.39999999999998
248.39999999999998
['.arrow', '0', '0', '0', '248.39999999999998', '0', '0', '16.56', '66.24']
> artiax particles #1.2.3 originScaleFactor 16.56
> artiax view xy
set axis size 248.39999999999998
248.39999999999998
['.arrow', '0', '0', '0', '248.39999999999998', '0', '0', '16.56', '66.24']
> artiax particles #1.2.4 originScaleFactor 16.56
> artiax view xy
set axis size 248.39999999999998
248.39999999999998
['.arrow', '0', '0', '0', '248.39999999999998', '0', '0', '16.56', '66.24']
> artiax particles #1.2.5 originScaleFactor 16.56
> artiax view xy
set axis size 248.39999999999998
248.39999999999998
['.arrow', '0', '0', '0', '248.39999999999998', '0', '0', '16.56', '66.24']
> artiax particles #1.2.6 originScaleFactor 16.56
> artiax view xy
> hide #!1.1.22 models
> hide #!1.1.21 models
> hide #!1.1.20 models
> show #!1.1.20 models
> hide #!1.1.19 models
> hide #!1.1.18 models
> show #!1.1.18 models
> hide #!1.1.18 models
> hide #!1.1.17 models
> show #!1.1.17 models
> hide #!1.1.17 models
> hide #!1.1.16 models
> show #!1.1.16 models
> hide #!1.1.16 models
> hide #!1.1.15 models
> show #!1.1.15 models
> hide #!1.1.14 models
> hide #!1.1.13 models
> hide #!1.1.12 models
> show #!1.1.12 models
> hide #!1.1.11 models
> show #!1.1.11 models
> hide #!1.1.11 models
> hide #!1.1.10 models
> show #!1.1.10 models
> hide #!1.1.10 models
> hide #!1.1.9 models
> hide #!1.1.8 models
> show #!1.1.8 models
> hide #!1.1.7 models
> hide #!1.1.6 models
> show #!1.1.6 models
> hide #!1.1.5 models
> hide #!1.1.4 models
> show #!1.1.4 models
> hide #!1.1.3 models
> show #!1.1.3 models
> hide #!1.1.2 models
> show #!1.1.2 models
> artiax hide axes
> artiax hide markers
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Class1_average_828_masked_64pix.mrc
Opened Class1_average_828_masked_64pix.mrc as #2, grid size 64,64,64, pixel
8.28, shown at level 0.214, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened Class1_average_828_masked_64pix.mrc as #1.2.1.1.1, grid size 64,64,64,
pixel 8.28, shown at level 0.214, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Class2_average_828_fatmasked_64pix.mrc
Opened Class2_average_828_fatmasked_64pix.mrc as #2, grid size 64,64,64, pixel
8.28, shown at level 6.87e-05, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened Class2_average_828_fatmasked_64pix.mrc as #1.2.2.1.1, grid size
64,64,64, pixel 8.28, shown at level 6.87e-05, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 color 30,0,36,100
> artiax particles #1.2.2 surfaceLevel 0.40632
> artiax particles #1.2.2 surfaceLevel 0.47244
> artiax particles #1.2.2 surfaceLevel 0.31817
> artiax particles #1.2.2 surfaceLevel 0.23002
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Class3_average_828_masked_64pix_dusted.mrc
Opened Class3_average_828_masked_64pix_dusted.mrc as #2, grid size 64,64,64,
pixel 8.28, shown at level 0.0657, step 1, values float32
> artiax attach #2 toParticleList #1.2.3
Opened Class3_average_828_masked_64pix_dusted.mrc as #1.2.3.1.1, grid size
64,64,64, pixel 8.28, shown at level 0.0657, step 1, values float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax particles #1.2.3 color 100,80,60,100
> artiax particles #1.2.3 surfaceLevel 0.21053
> artiax particles #1.2.3 surfaceLevel 0.31025
> artiax particles #1.2.3 surfaceLevel 0.29212
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Class4_average_828_masked_64pix.mrc
Opened Class4_average_828_masked_64pix.mrc as #2, grid size 64,64,64, pixel
8.28, shown at level 0.0185, step 1, values float32
> artiax attach #2 toParticleList #1.2.4
Opened Class4_average_828_masked_64pix.mrc as #1.2.4.1.1, grid size 64,64,64,
pixel 8.28, shown at level 0.0185, step 1, values float32
> volume #1.2.4.1.1 capFaces false
> artiax show #1.2.4 surfaces
> artiax particles #1.2.4 color 56,49,0,100
> artiax particles #1.2.4 surfaceLevel 0.36737
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/G2Class1_average_828_masked_64pix.mrc
Opened G2Class1_average_828_masked_64pix.mrc as #2, grid size 64,64,64, pixel
8.28, shown at level 0.246, step 1, values float32
> artiax attach #2 toParticleList #1.2.5
Opened G2Class1_average_828_masked_64pix.mrc as #1.2.5.1.1, grid size
64,64,64, pixel 8.28, shown at level 0.246, step 1, values float32
> volume #1.2.5.1.1 capFaces false
> artiax show #1.2.5 surfaces
> artiax particles #1.2.5 color 0,20,50,100
> open
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/G2Class4_average_828_masked_64pix_dusted2.mrc
Opened G2Class4_average_828_masked_64pix_dusted2.mrc as #2, grid size
64,64,64, pixel 8.28, shown at level 0.0999, step 1, values float32
> artiax attach #2 toParticleList #1.2.6
Opened G2Class4_average_828_masked_64pix_dusted2.mrc as #1.2.6.1.1, grid size
64,64,64, pixel 8.28, shown at level 0.0999, step 1, values float32
> volume #1.2.6.1.1 capFaces false
> artiax show #1.2.6 surfaces
> artiax particles #1.2.6 color 26,40,0,100
> artiax particles #1.2.6 surfaceLevel 0.2876
> hide #!1.1.15 models
> show #!1.1.15 models
> hide #!1.1.12 models
> show #!1.1.12 models
> hide #!1.1.20 models
> show #!1.1.20 models
> hide #!1.1.6 models
> show #!1.1.6 models
> save
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/Lam18ts2_trace.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/home/rezagull/.local/share/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/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 0x7f6ffccd0ee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f6fc867fa40> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/home/rezagull/.local/share/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/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 0x7f6ffccd0ee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f6fc867fa40> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/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.
> open help:user/artiax_index.html
Opened help:user/artiax_index.html
> save
> /media/rezagull/8TB/Jun10/imod/Jun8grid2_wbpBin4deconv/particlepick3/maskcreate/test.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/home/rezagull/.local/share/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/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 0x7f6ffccd0ee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f6fc867fa40> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/home/rezagull/.local/share/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/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/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/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 0x7f6ffccd0ee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f6fc867fa40> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/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 525.60.13
OpenGL renderer: NVIDIA RTX A6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 36 Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
Cache Size: 25344 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 45Gi 9.5Gi 417Mi 196Gi 202Gi
Swap: 0B 0B 0B
Graphics:
1a:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A6000] [10de:2230] (rev a1)
Subsystem: NVIDIA Corporation GA102GL [RTX A6000] [10de:1459]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
starfile: 0.4.11
superqt: 0.4.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (1)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArtiaX session save: Unknown class name 'MarkerSetPlus' |
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Reported by Reza Paraan