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

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

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Subject: Re: Building peptide in density using coot.
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-09-03

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From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2008-09-03

Subject: Re: Building peptide in density using coot.
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-09-03

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 --
> ------------------------------------------------------------
> 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: Re: Building peptide in density using coot.
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-09-03

Next message:
Subject: refining nucleic acid structures: Refmac or CNS?
From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2008-09-03