From: John Stone (
Date: Mon Apr 06 2015 - 10:59:53 CDT

  Do you want to draw the residues, or just get their IDs for use
in further analyses? If you just want to see them, you should be able
to use the "trajectory" tab and the "draw multiple frames" feature to show
the matching residues from multiple trajectory frames superimposed into a
single image. If you want to obtain a list of the VMD "residue or "resid"
tags for the residues in close proximity, you would obtain that list using
a loop over all of the trajectory frames. This can either be done using
the "bigdcd" script in the VMD script library, or if you just need to do
it over the trajectory frames currently loaded, you can do it with a
simple 'for' loop that updates the atomselection, e.g. via "$sel frame",
and "$sel update". There are many examples of thse kinds of analyses
in prior mailing list postings and in the various VMD tutorials available
on the VMD web site and across the internet.

  John Stone

On Fri, Apr 03, 2015 at 12:24:56PM -0400, Aryan Vahedi wrote:
> Hello,
> I am investigating the interaction of a protein with CNT. I have run a
> simulation for 100 ns and can see that the protein is adsorbing onto the
> surface on the CNT. Using the Graphical Representations GUI I can visually
> identify possible contact residues using the selection:
> protein and within 1.5 of resname CNT
> Then after choosing "Update Selection After Every Frameā** under
> Trajectory (in Graphical Representations) and setting an appropriate
> Drawing Method I can clearly see which atoms come into that distance over
> the course of the trajectory.
> My question is what is the series of command I can use in the Tk console
> to quickly identify these residues. I use:
> $sel1 get resid resname
> But this only gives me the selection (protein and within 1.5 of rename
> CNT) I made at a particular frame. What command can I use to identify
> (i.e. have them printed in the console) the residues that fall within 1.5
> A of the CNT over the course of the entire trajectory I have loaded in?
> Many Thanks for Your Help,
> Aryan Vahedi
> MS Biology
> Morgan State University

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