Hey Flávio,

It's a Python syntax problem. You have a leading space before those lines (all starting with rsr.add). Remember that in Python, white-space *is* important. Removing that space will make it work.

Cheers,

João [...] Rodrigues http://nmr.chem.uu.nl/~joao

On Sat, Jun 18, 2011 at 8:01 PM, flavio seixas oivalf_nix@yahoo.com wrote:

> Hi, > > I had sucessfull modelled a protein without restrains. > > However, when I put alpha helix restrains in the script below I face this > problem: > > > File "model-restriction-single.py", line 21 > rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:'))) > ^ > IndentationError: unindent does not match any outer indentation level > > > I saw the script too many times and I am not able to see where the problem > is. > > Could anyone help-me? > > > from modeller import * > > from modeller.automodel import * > > > > log.verbose() > > env = environ() > > > > env.io.hetatm = True > > > > # directories for input atom files > > env.io.atom_files_directory = ['.', '../atom_files'] > > > > > > class MyModel(automodel): > > def special_restraints(self, aln): > > rsr = self.restraints > > at = self.atoms > > > > # Add some restraints from a file: > > > > # Residues 47 through 57 should be an alpha helix: > > rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:'))) > > > > # Residues 130 through 140 should be an alpha helix: > > rsr.add(secondary_structure.alpha(self.residue_range('130:', '140:'))) > > > > # Residues 182 through 184 should be an alpha helix: > > rsr.add(secondary_structure.alpha(self.residue_range('182:', '184:'))) > > > > # Residues 191 through 195 should be an alpha helix: > > rsr.add(secondary_structure.alpha(self.residue_range('191:', '195:'))) > > > > > > > > a = MyModel(env, alnfile='MODEL-TemplateA.ali', > > knowns='TemplateA', sequence='MODEL', > > assess_methods=(assess.DOPE, assess.GA341)) > > a.starting_model = 1 > > a.ending_model = 5 > 0 > a.make() > > > > > > # Get a list of all successfully built models from a.outputs > > ok_models = filter(lambda x: x['failure'] is None, a.outputs) > > > > > > # Rank the models by DOPE score > > key = 'DOPE score' > > ok_models.sort(lambda a,b: cmp(a[key], b[key])) > > > > > > > > # Get top model > > m = ok_models[0] > > > > print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) > > m = ok_models[1] > > > > print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) > > m = ok_models[2] > > > > print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) > > m = ok_models[3] > > > > print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) > > m = ok_models[4] > > > > print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) > > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >