Clipper prevents session saving

[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
Trying to change contor levels.

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.  
  

> ui mousemode rightMode select

> ui mousemode rightMode clip

> show #!1.3 models

> ui mousemode rightMode "contour level"

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 458, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 387, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/map/mouselevel.py", line 23, in mouse_down  
self._maps = self._picked_maps(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/map/mouselevel.py", line 29, in _picked_maps  
return self._picked_maps_on_segment(xyz1, xyz2)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/map/mouselevel.py", line 37, in _picked_maps_on_segment  
mxyz1, mxyz2 = ppos * xyz1, ppos * xyz2  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
TypeError: Cannot multiply Place times "None"  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  




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

[Eric Pettersen]

Reported by Ken Satyshur

[Tom Goddard]

Fixed error using contour level mouse mode in stereo. Mouse modes were not working in stereo because there was no code to choose whether to line up the mouse pointer using the left eye or right eye. So no mouse modes that rely on mouse position over the graphics worked. I made it use the right eye.

A related tip for using stereo. Zooming with the scrollwheel with the Alt key held down will move the model z position relative to the screen. Without the Alt key it scales the model while keeping it at the same depth relative to the screen.

[Tom Goddard]

The first error in the log is a session save failure involving the Symmetry_Manger class. Reassigning that to Tristan who wrote that code. The Symmetry_Manager class either needs to declare it does not save in sessions or it add support for saving in sessions.

[Tristan Croll]

The latest versions of Clipper and ISOLDE no longer cause crashes on session saving, but are not yet fully saved. The atomic model will be returned on session restore, but other Clipper and ISOLDE-specific information is lost. Full save/restore capability will be added in a future release.