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.