VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Mar 10 2006 - 09:43:34 CST

Hi all,

I've been trying to visualize and save a bunch of structures from a
trajectory. What I'm trying to get is only the protein + a 5-A shell
of water around it and save it in a file. I'm using:

set prot5A [atomselect top "protein and (same residue as (resname TIP3
and within 4.0
of (protein)))"]

but it doesn't work. when I remove "protein and..." from the line, I
can visualize the shell of water, but that's all. I've tried to do it
from different ways, but I haven't succeed... Do you have any
suggestions?

Thanks!
Michel