Clipper not saving in sessions

[satyshur@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.1.2.el7.x86_64-x86_64-with-redhat-7.7-Maipo
ChimeraX Version: 0.91 (2019-09-30)
Description
Clipper display of electron density. Tried to save session.

Log:
UCSF ChimeraX version: 0.91 (2019-09-30)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6d52 format mmCIF fromDatabase pdb structureFactors true

Summary of feedback from opening 6d52 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for GLU #1 in chain B  
Atom H1 is not in the residue template for GLU #1 in chain D  
Atom H1 is not in the residue template for GLU #1 in chain C  
Atom H1 is not in the residue template for GLU #1 in chain A  
notes | Resolution: 1.4280533552397077  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
6d52 title:  
Superoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6
Angstrom resolution [more info...]  
  
Chain information for 6d52  
---  
Chain | Description  
1.3/A 1.3/B 1.3/C 1.3/D | Superoxide dismutase [Cu-Zn] 1  
  
Non-standard residues in 6d52 #1.3  
---  
CU — copper (II) ion  
ZN — zinc ion  
  
6d52 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> help help:user

> camera stereo

> camera mono

> camera stereo

> hide #!1.2 models

> show #!1.2 models

> hide #!1.3 models

> save session /instructor/satyshur/chimera-demo/SodCI/PDB-downloads-
peter/start-6d52.cxs

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 288, in process  
return copy_state(data, convert=convert)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 208, in copy_state  
return _copy(data)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 206, in _copy  
return convert(data)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 287, in convert  
return add_obj(obj, parents)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 882, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 612, in file_save_cb  
self.save_dialog.display(self, session)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 1089, in save  
run(session, cmd)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 981, in save_session  
save(session, filename, **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export  
result = self.export_func(session, path, **kw)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 288, in process  
return copy_state(data, convert=convert)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 208, in copy_state  
return _copy(data)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/state.py", line 206, in _copy  
return convert(data)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 287, in convert  
return add_obj(obj, parents)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.50
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

Reported by Ken Satyshur

[Tom Goddard]

Duplicate of #2458