Re: [PyMOL] Backbone RMSD

[Peter K. <ka...@AE...>]

Try this:

PyMOL>super PDBfile1////CA, PDBfile2////CA

PyMOL>Save PDBfile1.pdb, PDBfile1

PyMOL>Save PDBfile2.pdb, PDBfile2

Explanation:

The first line aligns the alpha carbons of the two files.I assume you 
have loaded the two files in advance. The RMSD will appear on the screen 
as output.The second and third lines take the Pymol objects PDBfile1 and 
PDBfile2 and saves their newly aligned coordinates in pdb format.You 
might want to look up the align and the super commands in the wiki.Super 
is a better version of align.

Super iterates, removing outlier atoms progressively until it finds no 
further statistical reason to remove any more.If you want only an 
alignment that uses all CA atoms, you can restrict the calculation to 
one iteration as follows:

PyMOL>super PDBfile1////CA, PDBfile2////CA, cycles=0

Then save the aligned files as above.

Peter Kahn



On 9/10/2014 12:11 AM, Amita Rani Sahoo wrote:
> Dear Pymol users,
>
> I want to calculate backbone RMSD of proteins having two different 
> conformations (For example 2RH1 and 1F88). With the align command it 
> calculates the executive RMSD, but i need backbone RMSD. Please advise 
> something.
>
>
>
> Regards
> *Amita *
>
>
>
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-- 
Peter C. Kahn, Ph.D.
Professor of Biochemistry
Department of Biochemistry & Microbiology
Rutgers University
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