[modeller_usage] Class mymodel: How to randomize coordinates

[Baptiste Legrand <>]

Hi all,

I try to make models from a template, with constraints (Helix) and a randomization of the coordinates for each models. I set deviation to 4.0 but MODELLER dont use it. A part of my script:

# Add Helix
class mymodel(automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        at = self.atoms
        rsr.add(secondary_structure.alpha(self.residue_range('2:', '13:')))
# Build models, and assess with both DOPE and GA341
a = mymodel(env, alnfile  = 'f125-1s35.ali',        # alignment filename (use default: 'a = automodel', 'loopmodel' for loop, 'allhmodel' to add protons)
                   knowns   = 
 '1j18',                 # codes of the templates (for multiple template, just add codes: knowns = ('1s35', '1quu'))
                   sequence = 'f3s5',                 # code of the target
                   deviation = 4.0,
                   assess_methods =(assess.DOPE, assess.GA341))   # assessment scripts
                  #inifile = 'my-initial.pdb')        # use my initial structure 

What should 
 I do to randomize in this case?
Thanks in advance,
Regards

Baptiste

---

Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail