Re: [ccp4bb] Building peptide in density using coot.

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Building peptide in density using coot.
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-09-03

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 --
------------------------------------------------------------
Chavas Leonard, Ph.D. @ home
Research Associate
Marie Curie Actions Fellow
------------------------------------------------------------
Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT
------------------------------------------------------------
Tel: +44(0)161-275-1586
e-mail: Leonard.Chavas@manchester.ac.uk
http://personalpages.manchester.ac.uk/staff/leonard.chavas/

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refining nucleic acids structure with Refmac
From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2008-09-03

Next message:
Subject: SUMMARY - Puzzling protein-protein interaction
From: Brett Collins b {- dot -} collins {- at -} IMB {- dot -} UQ {- dot -} EDU {- dot -} AU
Date: 2008-09-03