On 9 March 2011 15:44, Claudia Scotti claudiascotti@hotmail.com wrote:

> Dear Thomas, > > Many thanks for your suggestions. > > Yes: I have already tried to remove the alignment, but the "strand" does > not become a strand and it moves away from the beta sheet against which it > is supposed to pack. > > Mmhhh... Actually, should I try the beta sheet restraints? In this case, > please, I have some doubts on the command: >

It would be a good idea to try both the strand and beta sheet restraints and the leave this region unaligned.

> > rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'],sheet_h_bonds=-5)) > > Particuarly, please, I can't find the explanation of the syntax in > parenthesis. May you please help me with this? >

You mean the hydrogen bonding pattern in a beta sheet? Here is an explanation:

http://en.wikipedia.org/wiki/Beta_sheet#Hydrogen_bonding_patterns

and this one from Modeller's manual:

http://www.salilab.org/modeller/manual/node219.html

This is an example code snippet from my archive:

rsr.add(secondary_structure.strand(self.residue_range('1:', '7:'))) rsr.add(secondary_structure.strand(self.residue_range('19:', '26:'))) rsr.add(secondary_structure.strand(self.residue_range('56:', '63:'))) ##An anti-parallel sheet composed of the two strands: self.restraints.add(secondary_structure.sheet(at['N:2'], at['O:23'], sheet_h_bonds=-12)) self.restraints.add(secondary_structure.sheet(at['O:1'], at['N:59'], sheet_h_bonds=-8))

Good luck!

Thomas