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
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======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

tevang3@gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/