VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 06 2009 - 11:11:17 CDT

Hi,
  I would suggest assigning indices to the "beta" or "user" fields associated
with each atom, and coloring them either by the field containing the indices,
or by making multiple reps with selections for each grouping, and color them
by colorID. Either method, or a hybrid of the two, should work fine and would
do what you want with a single unified structure file. You can actually
write a script to generate the representations and selections for you,
so you don't have to paste anything at all in the GUI if you don't want to.
See the users guide, or play with "logfile console" to see the commands that
correspond to GUI actions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 06, 2009 at 10:43:05AM +0100, Stefano Meliga wrote:
> Hello vmd users,
>
> I use a clustering algorithm to find partitions of a protein with
> mechanical and dynamical meaning.
>
> I would like to visualise the protein and assign a colour to each cluster.
>
> At the moment I am loading the fragments of the pdb file corresponding
> to the clusters as different molecules and I use the colour category
> "molecule" to colour them.
> Unfortunately the different fragments are considered by VMD as different
> molecules so they are not joined together. Consequently the chain looks
> broken an some secondary structure are not recognised any more by
> NewCartoon and plotted as random coils.
>
> I wonder if I shall use the the "serial" keyword with the atom numbers
> to select them. This would imply to write a script to produce the
> sequence of atoms of a cluster in a line and the copy paste this line in
> the selected atoms field. Will I be able to do this having a line with a
> number of atoms up to a few thousands?
>
> Have you got a better idea?
>
>
> Cheers,
>
> Stefano 

-- 
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