[modeller_usage] A better way to do this?

[Stéphane Téletchéa <>]

Dear users,

I'm willing to create a peptide sequence from a fasta sequence, and add 
a disulfide bridge in it.

At the moment, my code "which works" is like this pseudo-code:

1 - create a model object, and model.build('sequence'), I am not 
applying any time of secondary structure constraint
2 - write this pdb (peptide.pdb)
3 - create a special align where target and template are identical 
(peptide.ali)
4 - create a new object, Mymodel derived from automodel to add the patch 
for disulfides
5 - generate models
6 - select the best one (peptide-cys.pdb)

I'm only willing to retrieve the "peptide-cys.pdb" file, can I bypass 
steps 2,3 and act directly on the initial model object created?

The implementation of the pseudo-code above is:

#####################################################################

# This demonstrates the use of alignment.append_sequence() and
# model.build_sequence() to build residue sequences from one-letter codes
# http://salilab.org/modeller/manual/node171.html

from modeller import *
from modeller.automodel import *

env.libs.topology.read('${LIB}/top_heav.lib')
env.libs.parameters.read('${LIB}/par.lib')

# Create a new empty alignment and model:
aln = alignment(env)
mdl = model(env)

mdl.build_sequence('ACAAAAACYAAAA')
mdl.write(file='pept.pdb')

class MyModel(automodel):
      def special_patches(self, aln):
        # The disulfide bridge is taken from the input sequence
        self.patch(residue_type='DISU', residues=(self.residues['2',
                                                  self.residues['8']))

a = MyModel(env,
            alnfile  = "tmppiralign.ali",
            knowns   = "pept",
            sequence = "pept-cys")

a.starting_model= 1
a.ending_model  = 10

a.make()

#####################################################################

tmppiralign.ali is of the form:

#####################################################################
>P1;pept
structureX:pept:1: :13: ::::
ACAAAAACYAAAA*
>P1;pept-cys
sequence:pept-cys::FIRST:@ END :::::
ACAAAAACYAAAA*
#####################################################################


Thanks a lot for corrections, suggestions,..

Stéphane

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