VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Apr 01 2005 - 14:11:32 CST

Hi,

- to calculate the rmsd between the structures and the average model
just choose the 'ave' option in rmsd or rmsdtt plugins.
- for the selections, you will have to find a common property (index,
resid, ...., look the vmd manual for more options) that defines the
selection you want. If you only have rna in the pdb files and they
residues are in the same order you might be able to use 'residue' for
the selection. If you cannot find any common property, just go to the
pdb files and renumber the residues to match each other.

Best,

Luis

gtg991m_at_mail.gatech.edu said the following on 04/01/05 12:17:

>Hello!
>
>I have 20 different RNA coordinate pdb files. I want to select some residues in
>each files. For example,
>1.pdb => resi 10-14
>2.pdb => resi 120-124
>3.pdb => resi 220-224
>...
>Then do the superimposition of all 20 RNA backbones within selections as above
>described to get the "average" model and then calculate RMSD between this model
>and each RNA.
>
>How to do that in VMD?
>
>Many thanks,
>
>Chiao
>--
>
>
>
> 

-- 
Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021
Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu