Re: [modeller_usage] query about coil region!!

[Jacob Glanville <>]

There is a way to enforce coil formation: manually modify the  
reference alignment so that the query is not aligned to the reference  
in the area of interest. Why do you want to do this?

Jacob Glanville
Informatics associate
Rinat Biotherapeutics and Bioinnovation Center; Pfizer Inc.
(415) 497-3552


On Aug 5, 2009, at 11:12 AM, Modeller Caretaker < 
> wrote:

> Cool Hunk wrote:
> > i really got it, can you please make me one more thing sure that  
> > can i
> > declare any part of my target a coil region irrespective of its
> > alignment wth template region, if yes then how?? cuz in tht example  
> > its
> > told about the helix n strand.... but not about coils...
>
> If the model is aligned with a template, you will get spatial  
> restraints
> that aim to constrain the model to look like the template. So if your
> template is a helix, and you try to add a strand secondary structure
> restraint, the two will conflict. So secondary structure restraints  
> only
> really work in regions of low sequence similarity.
>
> There is no "coil" secondary structure restraint, because "coil" is
> essentially the lack of any defined secondary structure. It's probably
> what you'll get by default in unaligned regions. There is no restraint
> that says "please don't form a helix or strand".
>
>    Ben Webb, Modeller Caretaker
> --
>              http://www.salilab.org/modeller/
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