AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Thu Oct 09 2008 - 22:23:48 CDT

Taufik,

You could do this using Jmol. It could be automated, but it wouldn't
necessarily be a "simple" method.

It would involve having some prepared templates for leucine and adenine,
doing a bunch of deletions, then a series of molecular rotations, appending
of atoms, and connecting of bonds. All those are pretty straightforward Jmol
capabilities now. But it would not be trivial.

Writing the file to disk would be a bit trickier, because you would want to
get the residues in the right order, renumber them, and lose the header,
probably.

But you would be the first person ever to do that....

Bob Hanson
Lead Developer, Jmol

On Thu, Oct 9, 2008 at 9:35 PM, <taufik.alsarraj_at_utoronto.ca> wrote:

> Hello,
> This is a general question.
>
> If i take a structure from the protein data bank, and the structure
> contains a protein and a DNA, is there a a software or a relatively simple
> method for modifying the protein sequence or the DNA sequence, e.g. changing
> an A to L (Protein) or changing a T to A (DNA). Short of manual modification
> in xleap or deleting the original DNA and creating a new one.
>
>
> Best,
> Taufik
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu