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