Re: [modeller_usage] Loop refinement: setting the right anchors in multichain models

[Jérôme Hénin <>]

Thanks Thomas, I will try this.

Jerome

On 26 April 2012 11:16, Thomas Evangelidis <> wrote:
> 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 <> 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
>> 
>> https://salilab.org/mailman/listinfo/modeller_usage
>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: 
>
>           
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
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>
>
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