VMD-L Mailing List

From: erik vogan (vogan_at_hwxtal.tch.harvard.edu)
Date: Wed Jun 21 2000 - 22:24:30 CDT

On Wed, 21 Jun 2000, Paul Hubbard wrote:

> Yet another semi-related question, but this is driving me nuts, so here
> goes...
>
> I would like to generate a ribbons digram of two molecules superimposed,
> each having their own colour. However, I would like a third colour (or
> transparent material) where they intersect.
>
> I can only get the front-most colour to show, and I can't find a program
> which can pick-out overlapping regions.
>
> Thanks for suggestions.

it's not _exactly_ what you want, but i used STAMP (you get it from
Geoff Barton's home page: http://barton.ebi.ac.uk/new/software.html)
(followed by molscript and then raster3d) to great effect in a similar
manner.

the basic proceedure is to generate the structural alignment with STAMP,
which as a portion of the proceedure outputs a molscript input file.
unfortunately, a seperate molscript input file is generated for each
aligned structure, but some simply concatenation of these files yeilds
the overlap you seek (as long as you are willing to use molscript).

other noteable points (from memory ... don't hold me precisely to these):
STAMP replaces "non-conserved" bits of the structures with coils
and traces. a quick
"egrep -v '(coil|trace)' input.molscript > conserved.molscript"
thus leaves you with only the conserved bits of secondary structure,
while retrieving the non-conserved bits of each structure takes a bit
more wizardry (or some hand editting).

you will also need to check STAMPs calls on "conservation", as two
residues of conserved "helix" hanging around in the middle of nothingness
might look a bit funny. STAMP tends to leave single residue bits of
beta sheet, or particularly funny trace bits. other than these quirks,
STAMP does an incredibly nice job, and i would highly recommend it.

best of luck !

erik vogan, Ph.D.
Laboratory for Molecular Medicine
Children's Hospital - Enders 673
320 Longwood Avenue
Boston, MA 02115 - USA
vogan_at_crystal.harvard.edu
phone: (617) 355-7372
fax (W): (617) 355-3506