[Chimera-users] Assisstance to claculate RMSD value

[Shreyas Iyer]

Okay thank you Sir.
I got it. Your guidance was really helpful.
Thank you.

On Fri, Oct 7, 2016 at 10:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Shreyas Iyer,
>
> You can compare related protein structures by superimposing them with
> MatchMaker (in menu under Tools… Structure Comparison) or its command
> version “matchmaker”.  This will give the RMSD in the Reply Log (menu:
> Favorites.. Reply Log).
>
> Description and instructions, graphical interface:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> matchmaker/matchmaker.html>
>
> …command, including examples:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
>
> Matchmaker uses only one atom per residue, the alpha-carbons (CA atoms).
> If you want to use more atoms or different atoms you would have to use the
> “match” command instead.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> P.S. The email address for Chimera questions is chimera-users at cgl.ucsf.edu
> (as CC’d here).
>
> On Oct 7, 2016, at 4:09 AM, Shreyas Iyer <shreyas.i.imsc14 at ahduni.edu.in>
> wrote:
>
> > Respected Sir/Madam,
> >
> > I wanted to know how to calculate RMSD values between any 2 homology
> models of a protein with the help of USCF Chimera. Please guide me as soon
> as possible.
> >
> > Awaiting a positive reply.
> >
> > Yours Sincerely,
> > Shreyas Iyer
>
>
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