VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 24 2012 - 10:33:23 CDT

Hi,
  There's actually an easy way to do this inside of VMD itself...
If you've got a volumetric dataset loaded in VMD, and you have an atom
selection, you can query the value (or interpolated value) of the volumetric
data at the location of each atom in the selection. For example:
  set sel [atomselect top all]

  # query the value of the nearest voxel of volumetric data 0,
  # at the location of each selected atom
  $sel get vol0

  # query the interpolated value of volumetric data 0, at the
  # location of each selected atom
  $sel get interpvol0

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 24, 2012 at 10:35:37AM +0200, raunest wrote:
> Dear Abolfazl,
>
> i have written an OpenDX to PDB converter -dx2pdb- It's part of the
> dxTuber package.
>
> After conversion the values / densities of each voxel are stored in the
> beta factor column of the pdb file.
>
> To use this converter you need to install dxTuber, which you can
> download from
> http://code.google.com/p/dxtuber/
> or
> http://www.csb.bit.uni-bonn.de/dxtuber.html
>
> cheers,
> Martin
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078