Subject: Re: [modeller_usage] a question on MODELLER usage
From: Modeller Caretaker <>
Date: Thu, 17 Jul 2008 16:48:58 -0700
Ivan Anishchenko wrote:
I deal with a peptide (35 residues long). I know its amino acid sequence
and a set of mean values for phi- and psi- dihedrals and the respective
confidence interval for each dihedral angle. The data is obtained from
the NMR experiments. The aim is to obtain a structure with the
main-chain dihedrals lying within the corresponding confidence interval
for every residue. Side chains can take any conformation. How can such
restraints be described in MODELLER?
1. Read in the initial structure (see the manual for complete_pdb) or
build an extended chain from the AA sequence (model.build_sequence).
2. Add restraints on each dihedral. See Restraints.add. To get the list
of atoms for each dihedral type in each residue, see Residue.phi and
Dihedral.atoms. For example, to constrain every phi angle in the model
'm' to 0 +/- 0.1 radians, using a Gaussian restraint:
for res in m.residues:
if res.phi is not None:
atoms = res.phi.atoms
f = forms.gaussian(group=physical.dihedral,
3. You may also want to build other sets of restraints, for example
stereochemical restraints. See Restraints.make.