[Chimera-users] RMSD after superimposition

Subhabrata Majumder, PhD subhabrata.majumder at saha.ac.in
Thu Jan 7 04:13:19 PST 2021

 Dear  Elaine,

 Thank you so much.

> 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

Subhabrata Majumder, PhD
Associate Professor E
Biophysics & Structural Genomics
Saha Institute of Nuclear Physics
Sector 1, Block AF
Kolkata -700064

Email subhabrata.majumder at saha.ac.in ;
       subhabrata.sinp at gmail.com

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