VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 20 2000 - 19:55:26 CDT

Hi Eric,
  We're glad you're finding VMD interesting already.

On Wed, Sep 20, 2000 at 03:49:07PM -0700, Eric Hu wrote:
> Hi, I'm a new user on VMD and am alrealy attracted by its amzing
> functions. Now I have a couple of questions.
> 1. How can I show the label of the residue name only ( not the atom name
> or chain name)?

VMD likes to put all of that info in the labels, to my knowledge there's
no way to limit this to just the residue name.

> 2. How can I hide the coordinate symbol at the left bottom corner in the
> display and export?

In the VMD "Display" form, change the pulldown selector named "Axes" from
"lower left" to "off". That will rid you of the axes. You can also create
a .vmdrc in your home directory with the command "axes location off", which
will disable them every time you run VMD from then on.

> 3. I don't quite understand how to select contact residues (14.6 in user
> menu). Let's say I have a protein.pdb file and want to define the
> contact residues with 200 GLU.

Being a computer scientist, I'm not familiar with what you mean by
"200 GLU", but I assume you mean resname GLU and resid 200, could
you elaborate? If you're looking for all residues in contact with
another residue ("200 GLU"?) you could do this:
  same residue as (all within 2 of (resname GLU and resid 200))

Does that answer your question?

  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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