VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 05 2005 - 19:00:45 CDT

Hi,
  Perhaps the right thing to do, since they are different structures and
the residue numbers you're comparing aren't the same among structures,
would be to write a Tcl script to collect the coordinates for each of
these different selections, and average them together. Once done, you
could load in a new copy of 1.pdb and assign the new averaged coordinates
to the 10-14 residue range, and align this modified 1.pdb section against
each of the others one at a time via scripting. Ugly, but I don't know of
a nice way to do this more automatically, at least assuming I'm understanding
your request correctly.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 01, 2005 at 12:17:21PM -0500, gtg991m_at_mail.gatech.edu wrote:
> 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
> --
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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