Re: make the helix longer

From: lily jin (lily1907_at_yahoo.com)
Date: Mon May 22 2006 - 15:19:57 CDT

Thanks for trying help. I want to keep the existing helix, and add one more turn at its end. For example:
  the sequence is
  
  1 TRYQQIDEDEAALFLTTTTKGKLTVERKTEMKTSGSTIK
  the existing structure is
  1 cccccccchhhhhhhhhhhhhhhhhhhhccccccccccc
  I want to make a tructure like:
  1 cccccccchhhhhhhhhhhhhhhhhhhhhhhhcccccc
  where 'c' means loop and 'h' mean helix
  I want to keep the structure for the first 28 residues intact, but the next four residues to continue the helix structure.
  Am I making it clear? Please let me know if still not. Thanks a lot!
  
hl332_at_drexel.edu wrote:i did not actually understand your question clearly. can you explain a bit more about it. If you want to remove a helix totally, you can always do it changing respective pdb file. You can delete whatever you wish to. But i guess you are thinking something else.please let me know.

Harish Vashisth
Graduate Student(Ph.D)
CAT-361,Department of Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: lily jin

Date: Monday, May 22, 2006 2:16 pm
Subject: namd-l: make the helix longer

> Hi,
> I have a helix of 4 turns in my structure. Now I want to prolong
> the helix into a five-turn helix. It is to say, change a fex
> residues in the loop next to the helix into an helix turn. How is
> it possible to do so with NAMD? Thanks a lot!
>
>
> Lily
>
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