VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 23 2005 - 12:58:50 CDT

Hi,
  Are you just interested in counting close contacts between lipids and
proteins characterized by their Z coordinate? If so, you should be able to
calculate something like this using a combination of the "within" atom
selection and something like "z > 5 and z < 6", or by doing the within,
and binning the results according to their Z coordinates. (i.e. select
all protein atoms within a given distance of the lipids, then from the
resulting selected protein atoms, add each atom to an appropriate Z
coordinate bin)
It'll take a bit of scripting, but one of these variations ought to get you
started. Perhaps someone else has already done something like this?

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 23, 2005 at 06:06:27PM +0100, syma wrote:
> Hi,
>
> I would really appreciate some advice on the following:
>
> I am running simulations of proteins in lipid bilayers. I would really like
> to analyse the number of lipid-protein interactions as a function of the z
> coordinate, ie would like to take a vertical slice bilayer.
>
> Is this possible/feasible with vmd?
>
> Thanks in advance,
>
> -Syma
>
> ***************************************************
>
> Dr Syma Khalid
> Lab. of Molecular Biophysics,
> Department of Biochemistry,
> University of Oxford
> South Parks Road,
> Oxford
> OX1 3QU
> U.K.
>
>
>
> ***************************************************
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078