On 11/25/2010 01:11 AM, Stéphane Téletchéa wrote: > 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)
That might work, although the restraints generated in step 4 would be all wrong (Modeller will be trying to make your models look like the extended chain you generated in step 1, but at the same time your disulfide patch will be trying to bring the pairs of CYS residues together). So even your best models will contain a *lot* of restraint violations.
Since you presumably have no structural information about your disulfide-bonded peptide, I would simply build the sequence in step 1 using model.build_sequence(): http://salilab.org/modeller/9v8/manual/node171.html
That function takes a special_patches argument, which is a user-provided function, so you can apply your DISU patches here.
Then I'd do some kind of optimization using simply stereochemical and van der Waals restraints, such as that at: http://salilab.org/modeller/9v8/manual/node253.html
Ben Webb, Modeller Caretaker