Dear Modeller,<BR><BR>I am trying to put secondary structure restraints (strand and sheet) to <BR>the MODELLER modeling. However, I found that most of the specified hydrogen-bonds<BR>between strands have not been satisfied in the final model. I understand<BR>that MODELLER tries to satisfy ALL the restraints and there<BR>may be some conflicts between my hydrogen-bond and other restraints.<BR><BR>My questions are: 1. do I have a way to make some restraints stronger than<BR>other restraints? 2. do I have a way to force some important restraints<BR>(like the beta-sheet) no matter whether they are conflicted with others?<BR><BR>Thank you very much!<BR><BR>The following is the python file I am using (please kindly point out <BR>any error in the file):<BR><BR>from modeller import *<BR>from modeller.automodel import *<BR>log.verbose()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<BR>env =
 environ()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<BR><BR><A href="http://env.io.at/" target=_blank><SPAN class=yshortcuts id=lw_1204517404_0><FONT color=#003399>env.io</FONT></SPAN></A>.atom_files_directory = './:../atom_files'<BR><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.append(file='distCA.rsr')<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('10:', '15:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('19:', '23:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('30:', '31:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 rsr.add(secondary_structure.strand(self.residue_range('39:', '41:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('44:', '49:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('55:', '66:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('69:', '74:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('78:', '85:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('93:', '94:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('98:', '101:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('110:', '116:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 rsr.add(secondary_structure.strand(self.residue_range('127:', '131:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.strand(self.residue_range('135:', '136:')))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['O:11'], at['N:23'],sheet_h_bonds=-4))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['O:20'], at['N:47'],sheet_h_bonds=-3))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['O:39'], at['N:115'],sheet_h_bonds=-2))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['O:44'], at['N:112'],sheet_h_bonds=-2))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['N:61'], at['O:71'],sheet_h_bonds=-2))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['O:56'], at['N:100'],sheet_h_bonds=-2))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 rsr.add(secondary_structure.sheet(at['N:70'], at['O:82'],sheet_h_bonds=-5))<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rsr.add(secondary_structure.sheet(at['O:81'], at['N:116'],sheet_h_bonds=-4))<BR><BR><BR>a = mymodel(env, <BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; alnfile='alignment.ali', <BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; knowns=('pdb1','pdb2','pdb3'), <BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; sequence='target',<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; )<BR>a.starting_model = 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<BR>a.ending_model = 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 &nbsp;<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<BR>a.make()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<BR><BR><p>&#32;

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