[Chimera-users] Chimera calculating RMSD

[ogochukwu ngozi]

 Thanks so much Elaine.
    On Monday, March 29, 2021, 12:08:37 AM GMT+8, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Dear Ogochukwu Nwaefulu,
There is a User Guide with explanations of just about every feature.  You can use the menu: "Help... Search Documentation" to search for terms, for example: RMSD.  That will give you links to parts of the User Guide.

As for your question, there are several related features for superimposing structures, and they also report the resulting RMSD value.  See this page for a summary, wth links to the detailed information on each, including "MatchMaker" and "Ensemble Match" tools and "match" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

There is also an "rmsd" command for if you do NOT want to superimpose structures on top of each other, but instead calculate the RMSD in their current positions.  That would be used, for example, to compare different positions of the same ligand but docked in different places on a receptor.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

Finally, there are several tutorials with examples of using these features.

This one includes MatchMaker:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>

This one has examples of using the "match" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html>

This one includes Ensemble Match:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>

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




> On Mar 27, 2021, at 11:20 PM, ogochukwu ngozi <blessedogo2000 at yahoo.com> wrote:
> 
> Dear Concerned,
> I am a PHD student from University Putra Malaysia. This is my first time using Chimera, please I need your assistance. I want to use chimera to calculate RMSD values, could you direct me on steps to take please? Thanks as I await your kind reply.
> Ogochukwu Nwaefulu
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