From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 14 2010 - 15:12:33 CDT

>From your description, it sounds like you're just wanting to replace
the coordinates of one with the coordinate from the other, in which case
you would do this:
  $s1 set {x y z} [$s2 get {x y z}]

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 14, 2010 at 10:26:14PM +0300, Mert Gür wrote:
> Dear all,
> I want to change only the carbon alpha coordinates of my vilin pdb
> file. The reason of doing that is to use the CA coordinates from a
> different pdb file as Targeted Molecular Dynamic target coordinates.
> I have two pdb files vilin.pdb which has all the initial coordinates
> and CA.pdb which only has the target CA coordinates. The residue index
> for the CA atoms is the same in both pdb file. However, atom indexes
> are different.
> Can anyone help me to change the CA coordinates in vilin.pdb to the
> ones in CA.pdb?
> Best,
> Mert
>
> mol load pdb vilin.pdb
> mol load pdb CA.pdb
>
> set s1 [atomselect 0 "name CA"]
> set s2 [atomselect 1 "name CA"]
> set s3 [atomselect 0 "protein"]
>
> I cant figure out the next step.

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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