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Re: [modeller_usage] query about coil region!!
- To: Modeller Caretaker <>
- Subject: Re: [modeller_usage] query about coil region!!
- From: Jacob Glanville <>
- Date: Wed, 5 Aug 2009 12:15:20 -0700
- Cc: Modeller Queries <>
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?
Rinat Biotherapeutics and Bioinnovation Center; Pfizer Inc.
On Aug 5, 2009, at 11:12 AM, Modeller Caretaker <
Cool Hunk wrote:
i really got it, can you please make me one more thing sure that
declare any part of my target a coil region irrespective of its
alignment wth template region, if yes then how?? cuz in tht example
told about the helix n strand.... but not about coils...
If the model is aligned with a template, you will get spatial
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
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
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