[Chimera-users] Straighten a helix

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 22 10:51:45 PDT 2009

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)
match #0:24-30 at n,ca,c,o #1:24-30 at n,ca,c,o
match #0:24-30 at ca #1:24-30 at 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:

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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