Hi all,<br><br>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:<br><br># Add Helix<br>class mymodel(automodel):<br>&nbsp;&nbsp;&nbsp; def special_restraints(self, aln):<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr = self.restraints<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; at = self.atoms<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.alpha(self.residue_range('2:', '13:')))<br># Build models, and assess with both DOPE and GA341<br>a = mymodel(env, alnfile&nbsp; = 'f125-1s35.ali',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # alignment filename (use default: 'a = automodel', 'loopmodel' for loop, 'allhmodel' to add protons)<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; knowns&nbsp;&nbsp; = 
 '1j18',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # codes of the templates (for multiple template, just add codes: knowns = ('1s35', '1quu'))<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; sequence = 'f3s5',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # code of the target<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; deviation = 4.0,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; assess_methods =(assess.DOPE, assess.GA341))&nbsp;&nbsp; # assessment scripts<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #inifile = 'my-initial.pdb')&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # use my initial structure <br><br>What should 
 I do to randomize in this case?<br>Thanks in advance,<br>Regards<br><br>Baptiste<p>&#32;



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