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
Display 6d52 in clipper with electron density. Wanted to save my work. Using daily build 10-1-2019 which does stereo correctly. Only in mono mode at the time. Center of density in stereo mode stays in the starting orientation and does not display correctly. Scaling is also at fault.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
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 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  
  
  

> hide #!1.2 models

> select up

Nothing selected  

> select up

Nothing selected  

> select down

Nothing selected  

> camera stereo

> camera mono

> show #!1.2 models

> camera stereo

> graphics restart

> close session

Deleting (LIVE) 2mFo-DFc_smooth_23  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc  
Deleting Crystallographic maps (6d52-sf.cif)  

> 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  
  
  

> camera stereo

> camera mono

> close session

Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_23  
Deleting Crystallographic maps (6d52-sf.cif)  

> 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  
  
  

> select #1.1.1.2

2 models selected  

> select clear

> select #1.1.1.2

2 models selected  

> select clear

> select #1.1.1.3

3 models selected  

> select clear

> select #1.1.1.3

3 models selected  

> select clear

> select #1.1.1.6

3 models selected  

> select clear

> select clear

> select #1.1.1.6

3 models selected  

> select #1.1.1.6

3 models selected  

> select #1.1.1.6

3 models selected  

> select #1.1.1.6

3 models selected  

> save session /disk1/satyshur/wustl-SSB/phenix/Refine_54/6d52-density.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 340.107
OpenGL renderer: Quadro FX 3800/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

Reported by Ken Satyshur

[Tristan Croll]

Duplicate of #2539