VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 21 2009 - 11:17:21 CDT

Hi,
  You might find the command "logfile console" to be very helpful
in constructing scripts to automate graphical representation setup..
Running "logfile console" will cause VMD to emit the text commands
that correspond to actions you perform in the graphical interface,
making it much easier to cut/paste them into your own scripts.
To turn it back off, you can use "logfile off".
The various representation commands are also documented fully
in the VMD User's Guide.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 21, 2009 at 12:01:19PM -0400, Myunggi Yi wrote:
> I found the way to add rep.
>
> mol selection {name "B.*" and segid 1}
> mol color ColorID 0
> mol rep DynamicBonds
> mol addrep 0
>
> Is there a way to specify the distance cutoff for dynamics bonds?
>
> On Mon, Sep 21, 2009 at 11:27 AM, Myunggi Yi <myunggi_at_gmail.com> wrote:
>
> Dear VMD users,
>
> I'd like to make a tcl script to load a molecule with trajectory in
> several graphic representations with different selections.
> I think I have seen some from the manual, but I can't find it.
>
> For example, I want to do
> > vmd -e load.tcl
>
> in load.tcl, I want to add several representations with
>
> name "B.*" and segid 1 (with dynamic bonds with a specific distance
> cutoff and color)
>
> Would anybody help me?
>
> --
> Best wishes,
>
> Myunggi Yi
> ==================================
> 91 Chieftan Way
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: +1-850-645-1334
>
> http://sites.google.com/site/myunggi/
> http://people.sc.fsu.edu/~myunggi/
>
> --
> Best wishes,
>
> Myunggi Yi
> ==================================
> 91 Chieftan Way
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: +1-850-645-1334
>
> http://sites.google.com/site/myunggi/
> http://people.sc.fsu.edu/~myunggi/ 

-- 
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