Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

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

Main steps:

   - Protein purification
   - Crystallisation

Special:

   - Programs for crystallography
   - X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

   - CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous 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		Next message:
Subject: Re: Building peptide in density using coot.
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-09-03


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

If your peptide has less than 400 atoms, you can also try and use the 'Fit
Ligand' option under the "Calculate" menu of the main window: read in the
coordinates of a peptide of the same length as the one you wish and use
"Simple Mutate" from the "Model/Fit/Refine" menu to adjust to the desired
sequence. Then choose "fit ligand" and click "flexible". That often works
amazingly well with decent density.

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Tue, 2 Sep 2008, Tarique wrote:

> Hi,
> 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.
>
> Tarique Khan
> Research scholar
> Structural Bilogy Unit,
> National institute of Immunology,
> Aruna Asaf Ali marg,
> new Delhi 110067
> India
> Open WebMail Project (http://openwebmail.org)
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous 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		Next message:
Subject: Re: Building peptide in density using coot.
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-09-03
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd