[Chimera-users] superimposing an all-atom structure to a reduced one

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 9 11:48:23 PST 2012

Hi Damien,
There must be some other problem.  I tried MatchMaker to superimpose an all-atom structure on a CA-only structure, and it worked.  Example:

open 1gix
del ~ :.w
open 2vqe
del #1 & ~ :.t
preset apply int 2
mm #0 #1

I also tried the other way around (mm #1 #0).  However, if you have a recipe for getting the problem, please use "Help... Report a Bug" in the Chimera menu and include instructions on how to reproduce it.  Thanks,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 9, 2012, at 9:41 AM, Damien Larivière wrote:

> Dear all,
> I have two instances of the same protein. One is the original pdb structure which has been locally deformed and saved as the second pdb structure.
> I would like to match the 2 pdb structures. However, one structure is a reduced version of the other in that it contains only the carbon-alpha trace plus one or two atoms of the side chain.
> I get an error message when I use MatchMatcher. What can I do to superimpose the all-atom structure onto the reduced one?
> Many thanks for your help!
> Damien
> ps: I can join the two pdb structures if necessary

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