From: Axel Kohlmeyer (
Date: Wed May 05 2010 - 21:39:54 CDT

On Wed, May 5, 2010 at 7:35 PM, Fatemesadat Emami <> wrote:
> Dear vmd users,
> I have several pdb files pertaining to different snapshots of one MD run
> (structures are exactly the same). Their names are in the format of
> SNAP1.pdb, SNAP2.pdb , ...
> I want to select first residue (e.g. LYS) of all them in one selection
> altogether; Is that possible.


> In fact, I want to add surf just around the first residue (I can do that
> with tcl one by one but take a bit of time for vmd to load 2000 files along
> with the surfaces).
> What I am using now is:
> for {set i 30} {$i < 2006} {incr i} {
>  set filename [concat SNAP$i.pdb]
>  mol new $filename waitfor all
>  mol representation surf 1
>  mol Material Glass1
>  mol selection {resname LYS}
>  mol addrep top
> }

i don't think this would make much sense.

if you are looking for some kind of density distiribution
over the trajectory - and your script looks like a *very*
crude version of that - you should have a look at the
volmap tool and then use an isosurface for the resulting
grid file. that is usually giving a much better representation
of what is happening then stacking 2000 transparent objects
on top of each other...


> I was wondering if I can improve doing that!
> Many thanks
> Fatima
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department
> The University of Akron

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.