[MMTK] Creating peptide from scratch

Konrad Hinsen research at khinsen.fastmail.net
Mon Jun 4 07:10:10 UTC 2012


Sabine Reisser writes:

 > i would like to create a peptide structure from scratch, basically 
 > defining the amino acid sequence and the termini (cyclic), and the 
 > secondary structure (beta sheet). I could create a PeptideChain  object 
 > but I couldn't figure out if there's a way to produce a pdb file with 
 > atomic positions (compare e.g. SwissPDBViewer which creates an ideal 
 > helix from an aa sequence).

MMTK does not create peptide chain structures from scratch, you have
to get them from the outside. I have use PyMOL to construct ideal
helices, which I then read into MMTK as PDB files. I think PyMOL
can create other secondary-structure motifs, but I can't say
if it can handle cyclic peptides.

Konrad.
-- 
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
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