id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 505 Molecular surface (coloring?) breaks session restore Elaine Meng Tom Goddard "I had a session with a molecule, molecular surface, and a dx file contoured at two levels as mesh. It saved without apparent error but could not be restored. Session file attached. If i remember correctly, the molecule was #2 and the dx file was #3. I'd had an MRC file open as #1 previously but closed it before saving the session. open /Users/meng/Desktop/3eebB-apbsdx.cxs format session Summary of feedbck from opening /Users/meng/Desktop/3eebB-apbsdx.cxs error Unable to restore session, resetting. Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/session.py"", line 481, in restore obj = sm.restore_snapshot(self, data) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molarray.py"", line 259, in restore_snapshot return cls(c_pointers) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molarray.py"", line 1023, in __init__ Collection.__init__(self, mol_pointers, AtomicStructure, AtomicStructures) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molarray.py"", line 112, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % str(type(items))) ValueError: Collection items of unrecognized type """" Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/session.py"", line 481, in restore obj = sm.restore_snapshot(self, data) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molarray.py"", line 259, in restore_snapshot return cls(c_pointers) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molarray.py"", line 1023, in __init__ Collection.__init__(self, mol_pointers, AtomicStructure, AtomicStructures) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molarray.py"", line 112, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % str(type(items))) ValueError: Collection items of unrecognized type """" During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/tool.py"", line 158, in execute cmd.run(cmd_text) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py"", line 2255, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py"", line 103, in open models = session.models.open(paths, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py"", line 351, in open session, filenames, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py"", line 368, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py"", line 328, in open_data models, status = open_func(session, stream, dname, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/session.py"", line 630, in open session.restore(input) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/session.py"", line 487, in restore self.reset() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/session.py"", line 361, in reset sm.reset_state(container, self) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py"", line 206, in reset_state self.remove([m for m in self.list() if not m.SESSION_ENDURING]) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py"", line 318, in remove parent = self._models[model_id[:-1]] KeyError: (2,) " defect closed blocker Input/Output fixed Eric Pettersen Tom Goddard all ChimeraX