VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 20 2007 - 13:05:25 CST

Hi,
  In order to use the Isosurface rep you'll have to specify which volume
data to render, that's a likely cause of your problem. For animating
potential maps the best solution at present is to use the Multiple Molcule
Animation plugin by Axel Kohlmeyer, as VMD doesn't (yet) support animated
volumetric data.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 20, 2007 at 12:40:59PM -0600, Cesar Millan wrote:
> Hi everybody I would like to do an animation of multiple potential maps of a
> protein using VMD. If I use the following script:
>
> ######################################
> set start 1
> set end 18
> set fileformat "frame%d_c.pqr"
> set fileformat2 "frame%d_c78.dx"
>
> set filename [format $fileformat [expr $start]]
> set filedx [format $fileformat2 [expr $start]]
>
> incr start
> puts "Reading initial frame in PDB sequence $filename"
> mol new $filename type pdb
> mol addfile $filedx type dx
> mol delrep 0 top
> mol representation Tube
> mol addrep top
>
> puts "Reading PDB files as an animation..."
> for {set i $start} {$i <= $end} {incr i 1} {
> set filename [format $fileformat [expr $i]]
> set filedx [format $fileformat2 [expr $i]]
> mol addfile $filename type pdb
> mol addfile $filedx type dx
> mol delrep 0 top
> mol representation Tube
> mol addrep top
> }
> ############################
>
> and the representation is Tube, Lines even MSMS the script works fine (I can
> see how the protein moves on the representation chosen) but if I change the
> representation to Isosurface the script failed (I just see an static map).
> If I load every conformation as a new protein and potential map and use
> Multiple Molecule Animation, I can see what I want.
>
> Does any one have any idea why the script is not working using Isosurface
> representation?
>
> Thanks a lot for any help.
>
> best regards. 

-- 
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