VMD-L Mailing List

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Mon Sep 21 2009 - 11:53:53 CDT

Thank you all.
I've got it from Tcl console function.

mol rep DynamicBonds 4.6 0.3 6.0

Have a great day.

On Mon, Sep 21, 2009 at 12:17 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
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/