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

[Elaine Meng]

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
focus

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
----------
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