Possibly by defining different chain IDs. To do that use the chain brake character "/" in your alignment and , for example, instead of writing this:
class MyLoopModel(dopehr_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('330:', '336:'))
write this:
class MyLoopModel(dopehr_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('330:A', '336:A'), self.residue_range('221:B', 22'8:B'))
HTH, Thomas
On 25 April 2012 22:16, Jérôme Hénin jhenin@imm.cnrs.fr wrote:
> Hi everyone, > > I am trying to do loop refinement on a multi-chain protein. My problem > is that Modeller tries to anchor C-ter loops to the N-ter of the next > chain, yielding unrealistic starting configurations, and making the > whole refinement fail. > > How can I instruct Modeller that the C-ter and the following N-ter > "loops" are to be modeled separately? > > Thanks, > Jerome > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >