VMD-L Mailing List

From: Fatemesadat Emami (fe2_at_zips.uakron.edu)
Date: Wed May 05 2010 - 18:35:26 CDT

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 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