Hi Francesco, You don't have to give the atom names for each residue, e.g. how about match #0:24-30 #1:24-30 (assuming these residues have equal numbers of atoms with the same names in the two structures) or match #0:24-30@n,ca,c,o #1:24-30@n,ca,c,o or match #0:24-30@ca #1:24-30@ca You may want to try the "iterate" option of the match command. You could use matchmaker instead of match, but that would use the whole chain rather than specific residues, so I doubt it fits your situation. Here is a discussion of the different ways to match things in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 22, 2009, at 10:32 AM, Francesco Pietra wrote:

Elaine: I have found a way to get a nearly perfect alpha helix from what was a bent alpha helix by imposing the phi and psi angles where they were out of the norm. However, both the barycenter and the orientation of the rectified helix have changed, so that it does no more fit its partners.

What I would like to do is using the Chimera "match" command to superimpose the rectified helix to the bent helix, then remove the bent helix and save pdb. Surely clashes will be there but perhaps not so many to hinder MD. Is there a short command to tell to Chimera to do the job without having to list atom per atom. The helix is long and trial and errors will be many...it is not laziness alone.

Or is anything better in Chimera than the match command? thanks francesco