On Mar 7, 2006, at 10:01 AM, Elaine Meng wrote:
Issue (2) can be even more taxing. IF the cofactor residue has the same name and its atoms have the same names and are in the same orders in all pairs of structures to be compared, you could then use EnsembleMatch. You'd specify the cofactor residue as the atoms to match, e.g. :fad (residues named FAD). Another approach in this situation would be to use the match command, e.g. command> match #1:fad #0:fad
As of Chimera 1.2184 and later, the restrictions aren't quite as onerous as Elaine outlined. The atom names still do have to correspond, but the atoms need not all be in the same order inside the residue. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu