VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 07 2005 - 16:11:13 CDT

Hi,
  We got your first message. It often takes several hours for
all of the VMD-L mails to make it out to all recipients, particularly
since the mailer gets stalled on several balky overseas mail servers.

Regarding your question:
  VMD assumes static connectivity information through the course of
a trajectory. For visualization purposes, we do provide a "DynamicBonds"
representation which has a user selectable distance based cutoff parameter.
Try out the DynamicBonds represenation and see if it does what you're
looking for.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 07, 2005 at 11:02:25PM +0200, Claire Zerafa wrote:
>
> ----- Original Message -----
> From: "Claire Zerafa" <cporteli_at_waldonet.net.mt>
> To: "'vmd list'" <vmd-l_at_ks.uiuc.edu>
> Sent: Wednesday, September 07, 2005 3:00 PM
> Subject: vmd-l: visualising bonds in vmd
>
>
> >Hi all,
> >
> >I am working with a protein (androgen receptor) ligand (steroidal & non
> >steroidal) complex. I have done some dynamics, and i want now to visualise
> >how bond formation with the ligand varies over time. I guess I should be
> >able to see this in vmd, in fact I can see the entire system move, but i
> >now want to focus on protein ligand interactions. How can I do this
> >please?
> >
> >claire 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078