id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2648 Atom.structure_category throwing exception is awkward goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-03) Description Atoms.structure_categories raises an exception if any atom does not have a category assigned. I think it should just give the string ""unassigned"" for those. Current exception makes it hard to use correctly for exampl to find all ligands would have to iterate through and check each atom instead of atoms[atoms.structure_categories == 'ligand']. Got this error trying zone mouse mode on markers (file attached). Previously reported in ticekt #2644. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-12-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/goddard/ucsf/chimerax/src/bundles/surface/test.cmm format markers Opened 1 marker sets containing 3 markers > ui mousemode rightMode zone Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 463, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 392, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/zone/zone.py"", line 216, in mouse_down self._show_zone(res) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/zone/zone.py"", line 52, in _show_zone nres = self._show_near_residues(residue, show_ligands=ribbon) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/zone/zone.py"", line 126, in _show_near_residues cats = all_atoms.structure_categories File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 195, in get_prop cget(self._c_pointers, n, pointer(values)) IndexError: Unknown structure category IndexError: Unknown structure category File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 195, in get_prop cget(self._c_pointers, n, pointer(values)) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.2.24 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. File attachment: test.cmm }}} [attachment:""test.cmm""] " enhancement closed normal Core fixed all ChimeraX