VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 02 2006 - 10:13:23 CDT

Enzo,
  If you don't like writing the long expression below, you could
simply do something like:

proc getatomcoords { index } {
  return [lindex [[atomselect top "index $index"] get {x y z}] 0]
}

You could then write the much more compact expression:
  getatomcoords 25

If you want to be able to specify the atom in a 1-based indexing scheme, you
could use "serial" rather than index, if you prefer:
proc getatomcoords { serial } {
  return [lindex [[atomselect top "serial $serial"] get {x y z}] 0]
}

You could then write the same command with 1-based indices:
  getatomcoords 26

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 02, 2006 at 04:39:10PM +0200, Enzo Vitale wrote:
> Dear VMD experts,
>
> I have another simple question, again related to scripting VMD by
> means of TCL: is there a predefined array variable holding the
> coordinates of all atoms of a given molecule ?
>
> So far, I get the coordinates via the following ugly expression:
>
> [lindex [[atomselect top "index 25"] get {x y z}] 0]
>
> when for instance I need the coordinates of the 26-th atom, but I
> guess there must be a simpler and more readable form for getting the
> same result.
>
> Thank you in advance,
> Enzo 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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