[Chimera-users] superimposing structures with Chimera

[Elaine Meng]

> On Feb 10, 2022, at 1:42 PM, Kaina Quintero Chavez <kaina.quintero at uabc.edu.mx> wrote:
> 
> Hi, My name is Kaina. I am a current college student in UABC. I am currently doing my thesis in biology and came upon using UCSF chimera and am in a stuck position on how to use the superimpose feature. I was hoping you can guide me or reference me to a workshop/ course? anything really to get the job done.
> Thanks, hope to here from you.
> -- 
> Kaina


Hi Kaina,
We usually recommend the chimera-users at cgl.ucsf.edu address for asking questions -- I CC'd it here, hope that's OK.  Also it would be helpful to include more information when you send a question, like what you are trying to superimpose, what you tried already, what problem(s) caused you to be stuck, etc... but I will try to answer below.

There are lots of different ways to superimpose structures in Chimera and it depends on your situation as to which one you would use.  There is a discussion of the different ways here:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

If you have atomic structures of proteins or nucleic acid chains, probably the easiest approach is to try using the Matchmaker tool, menu: Tools... Structure Comparison... Matchmaker.  You would choose one structure as the reference and the other one as the one to match, and then just click "Apply" to see if the default settings work. 

Here is the help for Matchmaker
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

...and this tutorial includes examples of using it
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>

There is also a "matchmaker" command that does the same thing, and the help includes some example commands:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

However, maybe your situation is different and you would need to use one of the other methods discussed in the first link above.

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