Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement

- 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: POST DOCTORAL POSITION IN STRUCTURAL ENZYMOLOGY AND INHIBITOR DESIGN
From: Steve Almo almo {- at -} MEDUSA {- dot -} BIOC {- dot -} AECOM {- dot -} YU {- dot -} EDU
Date: 2007-06-22

Next message:
Subject: Suse 10.2 install problem
From: John Bruning jbruning {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-22

Subject: Re: Ligand fitting in COOT and SHELX refinement
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-06-22

You can use SHELXPRO to generate ligand restraints, reading in the ligand
from the CSD or as a SHELX file (which if necessary can be generated from
a PDB file using SHELXPRO). You may have to add some extra restraints by
hand (e.g. FLAT, CHIV).

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582

On Fri, 22 Jun 2007, U Sam wrote:

> Hi
> I would like to know following issue for a ligand.
> A ligand of a long alkyl chain can have multiple conformation.
> In coot in order to fit any protein residues into "difference Density", we can select a specific "rotamer" conformation and refine.
> For fitting ligand of above kind, how does it work out.
> Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature.
> I appreciate suggestion and comments.
> Many Thanks
> Sam
> _________________________________________________________________
> With Windows Live Hotmail, you can personalize your inbox with your favorite color.
> www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607

CCP4bb navigation

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

Next message:
Subject: Suse 10.2 install problem
From: John Bruning jbruning {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-22