Re: [modeller_usage] Beta strand

On 9 March 2011 15:44, Claudia Scotti <">> 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