[Chimera-users] Structure overlay

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 10 17:26:53 PDT 2019

Dear Joydeep,
When you first open structures, Chimera just uses the x,y,z coordinates in the input files; it does not automatically superimpose (overlay) similar structures.  Although the structures look almost superimposed, they could probably be superimposed better, so you could try doing that with the Matchmaker tool (menu: Tools… Structure Comparison… Matchmaker).

Different ways to superimpose structures in Chimera are listed here:

See also the tutorials, for example “Superpositions and Alignments”:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 10, 2019, at 8:24 AM, Chakraborty, Joydeep <jc323 at njit.edu> wrote:
> Dear all,
>   I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure.
>   I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue.
> Thanks,
> Joydeep.
> <MS Actv site pocket.pptx>

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