VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 07 2006 - 13:49:27 CDT

Hi,

On Thu, Jul 06, 2006 at 02:39:22PM -0500, Urahata wrote:
> Hi all,
>
> I appreciate if anyone could shed some light or point out to the right
> direction
> for three basic operational questions regarding VMD.
>
> 1. We have a box with one protein solvated by explicit water. We want to
> show water molecules that are within a distance range from one residue.
> It is not just the closest waters but only the ones located between
> distances
> r and r+dr. Let's say that the range is defined by 5A and 8A. I tried :
>
> water within 8A of resname PHE and not water within 5A of resname PHE
>
> but that's not the right way.

I don't have time to work it out for you just this second (imminent meeting),
but you should be able to do this with the correct atom selection syntax.
Let me know if you still need help with this.

> 2. Is it possible to load two (close) atoms without having VMD
> (automatically) building
> a bond between them ?

Not if you load them in a file that doesn't specify bonds (such as a PDB).
If you want to show all of the atoms within a particular distance of a
particular atom over the course of a trajectory, it is easier to do this
using the "draw multiple frames" frame selection box in the Trajectory
tab of the graphical representations window. There's no need to create
a modified structure in order to see the superposition of atoms over time...
I assume you already have the trajectory, so this should be easy.
 
> 3. Is it possible to load, let's say, water density in some sort of grid
> for later renderization ? This would lead to the same goal of question 2,
> without loading too many overlapping points/sites.

Yes, see the Extensions->Analysis->VolMap Tool extension for a tool to
create density maps from time averaged spatial occupancy etc...

  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