VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 28 2003 - 14:18:12 CST

Rudesh,
  This is easy to accomplish by writing a short Tcl script to calculate
the distances of the two sets of atoms via atom selections. You can query
the xyz positions of the atoms with '$sel get x y z' for example. There
are a few scripts you can look at in the script library that do various
forms of this sort of thing:
  http://www.ks.uiuc.edu/Research/vmd/script_library/

Look at this one to see the atom selection code of interest:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/ca-dist-v2.0/

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 28, 2003 at 04:32:51PM +0000, Rudesh Toofanny wrote:
> Hi,
>
> I want to monitor the distances between two sets of atoms in a protein during the course of a trajectory (.dcd file), is there a way to do this? I know you can do a similar thing with 'measure contacts' for single frames or a pdb file.
>
> Many thanks,
>
> Rudesh
>
> ________________________________________
> Rudesh Toofanny
> EPSRC PhD Student
> Laboratory of Biophysics and Surface Analysis
> Computational Modelling and Informatics Group
> The Boots Science Building
> School of Pharmacy
> University of Nottingham NG7 2RD
> tel: +44 (0)115 8466272
> fax: +44 (0)115 9615110
> http://www.nottingham.ac.uk/lbsa 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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