Hi, <div>I try to refine a long loop in my protein model by adding several secondary structure restraints and I&#39;ve confronted the following problem: some restraints do not have any effect unless other ones are removed from the restraint list. In other words, after removing some of the restraints others start working properly. I would like to know the reasons and how can this problem be solved. </div>
<div>I use the following script: </div><div><div><br></div><div>from modeller import *</div><div>from modeller.automodel import * # Load the automodel class</div><div>log.verbose()</div><div>env = environ()</div><div># directories for input atom files</div>
<div>env.io.atom_files_directory = [’.’, ’../atom_files’]</div><div>class MyModel(automodel):</div><div>def special_restraints(self, aln):</div><div>rsr = self.restraints</div><div>at = self.atoms</div><div># Add some restraints from a file:</div>
<div># rsr.append(file=’my_rsrs1.rsr’)</div><div># Residues 20 through 30 should be an alpha helix:</div><div>rsr.add(secondary_structure.alpha(self.residue_range(’20:’, ’30:’)))</div><div># Two beta-strands:</div><div>rsr.add(secondary_structure.strand(self.residue_range(’1:’, ’6:’)))</div>
<div>rsr.add(secondary_structure.strand(self.residue_range(’9:’, ’14:’)))</div><div><br></div><div>a = MyModel(env, alnfile = ’alignment.ali’, knowns = ’5fd1’, sequence = ’1fdx’) </div><div><br></div><div>a.starting_model= 1 </div>
<div>a.ending_model = 1 </div><div><br></div><div>a.make()                 </div></div><div><br></div><div>Thank you for attention. <br clear="all"><br>-- <br>Lilit Nersisyan<div>Institute of Molecular Biology NAS RA <br>
<div>E-mail: <a href="mailto:txgt.lilit.nersisyan@gmail.com" target="_blank">txgt.lilit.nersisyan@gmail.com</a></div><div>Tel.: +37494 601703</div></div><br>
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