FastVolumeSurface class not restorable

[n.keep@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
note | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 98, in _build_bundle  
bundle_d = d["bundle"][bundle_name]  
KeyError: 'ChimeraX_Clipper'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open "D:/Ann and Nick/Downloads/3io0-sf.cif"

> open "C:\Users\Ann and Nick\Desktop\test.pdb"

File not found: C:\Users\Ann and Nick\Desktop est.pdb  

File not found: C:\Users\Ann and Nick\Desktop est.pdb  

> open "C:/Users/Ann and Nick/Desktop/test.pdb"

Summary of feedback from opening C:/Users/Ann and Nick/Desktop/test.pdb  
---  
warning | Ignored bad PDB record found on line 3846  
END  
  
test.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for test.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  

> toolshed show ISOLDE

test.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for test.pdb  
---  
Chain | Description  
1.3/A | predicted microcompartment protein  
  

could not retrieve bundle list from toolshed  

Unknown command: backgorund white  

Unknown command: background white  

> set bgColor white

> help help:user

Developer warnings in user commands index:

  * didn't expect href to be to tools/sequenceviewer.html on line 245

  

> save session F:/CCP4PROJECT/chimerarebuild.cxs

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

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 791, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 564, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 141, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 40, in save  
return self._save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 93, in _session_save  
run(session, "save session %s" % quote_if_necessary(filename))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 917, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 198, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 730, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 500, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 265, in process  
return copy_state(data, convert=self._add_obj)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 174, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 172, in _copy  
return convert(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of FastVolumeSurface 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 FastVolumeSurface class in
ChimeraX-Clipper bundle because the class name is not listed in the name to
class table for session restore  
  
File "C:\Program Files\ChimeraX\bin\lib\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: 3.3.14009 Core Profile Forward-Compatible Context 21.19.142.257
OpenGL renderer: AMD Radeon(TM) R7 Graphics
OpenGL vendor: ATI Technologies Inc.

[tic20@…]

Hmm, yes - I’m afraid I haven’t done anything yet to make ISOLDE compatible with ChimeraX’s session save/restore. Partly because I simply haven’t had time, partially because I’ve been waiting until that component of the ChimeraX API is stable. It’s probably about time I started rectifying that. Eric: do you have anything I can look at for pointers?
 

 

[Tristan Croll]

Clipper and ISOLDE no longer break session saving (note - they don't actually *save* themselves yet, but they don't prevent other things from saving and you'll still get your model back on reloading). Full save/restore capability is in development.