VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 29 2008 - 13:13:24 CDT

Hi,
  Try the command again like this:
set sel [atomselect top nitrogen]
volmap occupancy $sel -res 0.2 -allframes -combine max -mol top

To show the newly created data, you must create a new isosurface
representation either with the graphical representations window,
or by text commands, e.g.:
mol color Name
mol selection all
mol material Opaque
mol addrep top
mol modstyle 1 top Isosurface 0.500000 0.000000 0.000000 0.000000 1 1

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 29, 2008 at 08:55:49AM -0400, Kaur, Tarandeep wrote:
> I am trying to use volmap tool to create an occupancy map. I want the
> occupancy of Nitrogen. It works fine if I use the GUI. However if I try
> to write a command at the vmd prompt it does not show anything or just
> draws a box around the compound. Also if I try to use the command in a
> tcl script it draws a box and does not take all frames in account. In
> the tcl script it shows total frames = 1 when actually there are 50
> frames. The command I am executing is
>
> volmap occupancy [atomselect top nitrogen] -res 0.2 -points -allframes
> -combine max -mol top
>
> I am executing in windows.
>
> Please help
>
>
>
> Tarandeep
>
>
> 

-- 
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