Hi -
If you could compromise to do it outside coot you could also:
a. Use "ARP/wARP Ligand Build" and treat the peptide as a ligand (if
its not too big)
b. Use "ARP/wARP Loops" if its a missing loop (a part of a bigger
chain).
Both should also work well at 2.1 A.
Tassos
On Sep 3, 2008, at 7:34, Chavas Leo wrote:
Dear Tarique --
On 2 Sep 2008, at 12:58, Tarique wrote:
Can any body tell me how to build peptide fragment of 5-6 residues
using
coot,if the sequence is known.I am working at 2.1 angstroms
resolution map.
If the peptide you're trying to build is a loop, and the density is
visible, you can use the Fit Loop option, straight forward to
understand. Now, if you're trying to build a peptide not related to
your protein, e.g. a ligand, I would start by importing a single
alanine.pdb file that would contain the coordinates for an alanine,
place the alanine in the density you can see, and start to build
from it. You can still mutate with the proper amino acids later on.
Please note that I'm still working on an hold version of Coot,
without any fancy additional options :)
HTH
Kind regards.
-- Leo --
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Chavas Leonard, Ph.D. @ home
Research Associate
Marie Curie Actions Fellow
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The University of Manchester
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M13 9PT
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