[Chimera-users] superimposing non-biopolymers

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 13 10:18:56 PST 2013

Hi Noel,
It sounds like you were trying to use MatchMaker, which (as you said) is only for superimposing biopolymer chains.  Instead you would need to use the "match" command, which lets you specify exactly which atoms to use in the fit.

See discussion of the different ways to superimpose structures in Chimera:

...and specifically the "match" command:

I hope this helps,
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 12, 2013, at 6:22 PM, Noel Pace wrote:

> Hi again Elaine,
> I have a second question apart from the Utility enquiry. 
> I would like to first superimpose different SDF files (e.g. 1.sdf, 2.sdf, 3.sdf) of the same molecule [Biotin: a small molecule and not a protein] and then show conformational changes from one SDF to the other. However the program is not letting me do this as the molecules do not contain nucleic or amino acids. 
> How can I do this with commands?
> Thanks again,
> Noel

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