id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 536 """split atoms atomspec"" gives traceback" Elaine Meng Tom Goddard "I was originally testing whether the ""atoms"" keyword could be given multiple times like it can in Chimera (see http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html ), but that gives an error. Then I tried just using it once, but that gives a traceback. (This command may be experimental anyway, prioritize as desired.) Example: open 2gbp split atoms :1-10 Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX.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/meng/Desktop/ChimeraX.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/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/split.py"", line 47, in split clist = split_molecule(m, chains, ligands, connected, atoms) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/split.py"", line 78, in split_molecule pieces = split_pieces(pieces, lambda a,atoms=atoms: split_atoms(a,atoms)) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/split.py"", line 92, in split_pieces splist = split_function(atoms) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/split.py"", line 78, in pieces = split_pieces(pieces, lambda a,atoms=atoms: split_atoms(a,atoms)) File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/split.py"", line 166, in split_atoms asubsets = [tuple(a for a in asub if a in aset) for asub in asubsets] File ""/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/split.py"", line 166, in asubsets = [tuple(a for a in asub if a in aset) for asub in asubsets] TypeError: 'Atom' object is not iterable " defect closed major Structure Editing fixed all ChimeraX