[PyMOL] building peptides

[Alan <ala...@gm...>]

Hello List,

I would like to have any help.

I want to build several 3-peptides, like AAA, FFF, KKK etc. I also
would like to make them zwitterionics, add chain and save as a PDB
file.

I know how to do that using the graphic interface, but I what I am
looking for is a way to do it via pymol script.

Is is possible? May anyone give a idea of how create the 3-peptides
and put right N- and C- terminals?

BTW, a loop with "for" is possible in pymol scripting?

Summarising, I am trying a script like this:

-----------------------
residue =3D ( ALA, ARG, etc)

for res in residue:
  'create peptide res-res-res'
  'set NH3 in res 1 and COO- in res 3'

save aa.pdb, all
-----------------------

Thanks a lot for any help.

Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.