id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1297 Handle tinyarray in session save/restore goddard@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-09-11) Description Using the zone mouse mode and saving session causes an error and session is not saved. Caused by View center of rotation set to a tinyarray which is not handled by session saving. Need session saving to handle tinyarray values. Currently trying to save a tinyarray in a session raises an error and session saving fails, and it is difficult to figure out where the tinyarray comes from. Log: UCSF ChimeraX version: 0.8 (2018-09-11) How to cite UCSF ChimeraX open 1a0m format mmCIF fromDatabase pdb ↵ 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...;] Chain information for 1a0m #1 --- Chain | Description A B | α-conotoxin [TYR15]-epi ui mousemode rightMode zone ↵ save test.cxs ↵ Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. Traceback (most recent call last):   File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 205, in execute     cmd.run(cmd_text)   File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2561, in run     result = ci.function(session, **kw_args)   File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/save.py"", line 61, in save     fmt.export(session, filename, fmt.nicknames[0], **kw)   File ""/Users/goddard/ucsf/chimerax/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 ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py"", line 717, in save     session.save(output, version=version)   File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py"", line 490, in save     mgr.discovery(self._state_containers)   File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py"", line 234, in discovery     self.processed[key] = self.process(obj)   File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py"", line 265, in process     return copy_state(data, convert=self._add_obj)   File ""/Users/goddard/ucsf/chimerax/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 ""/Users/goddard/ucsf/chimerax/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 ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/state.py"", line 159, in     items = [(_copy(k), _copy(v)) for k, v in data.items()]   File ""/Users/goddard/ucsf/chimerax/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 ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/session.py"", line 240, in _add_obj     uid = _UniqueName.from_obj(self.session, obj)   File ""/Users/goddard/ucsf/chimerax/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 tinyarray.ndarray_float RuntimeError: No bundle information for tinyarray.ndarray_float File ""/Users/goddard/ucsf/chimerax/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__)) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Sessions fixed Eric Pettersen all ChimeraX