VMD-L Mailing List

From: Stefano Meliga (smeliga_at_gmail.com)
Date: Thu Aug 06 2009 - 04:43:05 CDT

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