Hi Bala, No, I can't think of any way to specify the ring as a whole but with a stereotyped ordering of atoms. As far as I know, you would either have to specify the atoms individually (such as by name) in order in the command, or "pick" them in the Chimera window one by one, first all of the atoms of interest from one molecule and then from the other in the corresponding order, then specify your ordered selection in the command with the word "sel" or "selected" or "picked" Atom name approach, example commands: open pubchem:379413 open pubchem:25043 label match #1@o1,n3,n4,c10,c9,c8,c7,c12,c11 #0@o1,n1,n2,c3,c2,c1,c6,c5,c4 (The last command, match, should be all one line... the mail program may break it up. Also you might be using the rmsd command instead of match.) Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 2, 2012, at 6:59 AM, Bala subramanian wrote:

Friends, I have two ligands with a common benzoxadiazole ring. I want to do the rmsd comparison only on the ring, but the names of the atoms forming the benzoxadiazole ring are different in both the ligands.

Is there any way to use ring name as a string the compare the rmsd. ie. rmsd of benzoxadiazole of ligand 1 and benzoxadiazole ring of ligand 2

-- C. Balasubramanian