[Chimera-users] RMSD after superimposition

[Elaine Meng]

Hi Subhabrata,
You can get the CA RMSD per position from superimposed structures if you are showing a sequence alignment window. In the sequence alignment window, you can show the RMSD header (histogram) above the sequences and then save the values in that histogram using the sequence window Headers menu.

Of course, if you have only two structures superimposed, the CA "RMSD" at each position is simply the distance between the two CA atoms.

How to get the sequence alignment window: If you used Matchmaker to superimpose them, there is an option in the dialog to show each pairwise alignment, or if you used the matchmaker command, option "show true."  If you have more than two structures superimposed, you would need to use the Match->Align tool to make a multiple sequence alignment.  These tools are in the menu under Tools... Structure Comparison.

Details of showing and saving the header (and links to the manual pages of these tools) are given in previous posts, for example:
<https://www.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005629.html>

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

> On Jan 5, 2021, at 11:53 PM, Subhabrata Majumder, PhD <subhabrata.majumder at saha.ac.in> wrote:
> 
> Dear Support,
> I  have recently started using chimera_ucsf. I was trying to look at
> Calpha RMSD list after superimposition two conformation of a particular
> protein. Do you know where should I get the list after superimposition?
> Thanks,
> Subhabrata