Can't save ChimeraX session

[hyokeun.cha@…]

Hello,

I tried to save my ChimeraX session and got an error. Any way to get around this?

Thank you,
Michael



Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX.

Error in saving session for "CustomizedInstanceManager":
Traceback (most recent call last):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 253, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/attr_registration.py", line 159, in take_snapshot
return { 'instances': [inst for inst in all_python_instances()
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/attr_registration.py", line 160, in <listcomp>
if inst.has_custom_attrs and getattr(inst, 'session', None) == session] }
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molobject.py", line 803, in has_custom_attrs
return has_custom_attrs(Residue, self)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molobject.py", line 80, in has_custom_attrs
for attr_name, attr_info in klass._attr_registration.reg_attr_info.items():
AttributeError: type object 'Residue' has no attribute '_attr_registration'


Unable to save "CustomizedInstanceManager". Session might not restore properly.

Traceback (most recent call last):
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/gui.py", line 703, in <lambda>
    save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess))
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/gui.py", line 490, in file_save_cb
    self.save_dialog.display(self, session)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/save_dialog.py", line 141, in display
    fmt.save(session, filename)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/save_dialog.py", line 40, in save
    return self._save(session, filename)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/save_dialog.py", line 93, in _session_save
    run(session, "save session %s" % quote_if_necessary(filename))
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/run.py", line 31, in run
    results = command.run(text, log=log)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py", line 2622, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 896, in save_session
    save(session, filename, **kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/save.py", line 63, in save
    fmt.export(session, filename, fmt.nicknames[0], **kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py", line 198, in export
    result = self.export_func(session, path, **kw)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 715, in save
    session.save(output, version=version)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 488, in save
    mgr.discovery(self._state_containers)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 232, in discovery
    self.processed[key] = self.process(obj)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 263, in process
    return copy_state(data, convert=self._add_obj)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/state.py", line 172, in copy_state
    return _copy(data)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/state.py", line 159, in _copy
    items = [(_copy(k), _copy(v)) for k, v in data.items()]
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/state.py", line 159, in <listcomp>
    items = [(_copy(k), _copy(v)) for k, v in data.items()]
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/state.py", line 159, in _copy
    items = [(_copy(k), _copy(v)) for k, v in data.items()]
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/state.py", line 159, in <listcomp>
    items = [(_copy(k), _copy(v)) for k, v in data.items()]
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/state.py", line 170, in _copy
    return convert(data)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 238, in _add_obj
    uid = _UniqueName.from_obj(self.session, obj)
  File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 128, in from_obj
    obj_cls.__module__, obj_cls.__name__))
RuntimeError: No bundle information for chimerax.atomic.pbgroup.PseudobondGroup

RuntimeError: No bundle information for chimerax.atomic.pbgroup.PseudobondGroup

File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/session.py", line 128, in from_obj
obj_cls.__module__, obj_cls.__name__))

[Eric Pettersen]

Hi Michael,

It seems that you are using an older version of ChimeraX. Could you try upgrading to the 0.7 release or the daily build and see what happens. Also, if you still have problems it is much easier for me to debug the problem if you are using a more recent version...

--Eric

Eric Pettersen
UCSF Computer Graphics Lab