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

Re: [ccp4bb] nad woes - yet another question regarding ligand restraints
- 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: Re: nad woes
From: Thomas Edwards TEdwards {- at -} DECODE {- dot -} COM
Date: 2009-03-19		Next message:
Subject: import scaled failed on ccp4-6.1.1 but finished on ccp4-6.1.0
From: Jun Dong dong {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-03-19


Subject: Re: nad woes - yet another question regarding ligand restraints
From: Boaz Shaanan bshaanan {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2009-03-19

Is there a chance that  ThDP (TDP or TPP in the ccp4 dictionary) is restrained differently in 6.1.x than it used to be in 6.02 or even earlier versions (e.g. 5.2) ?

         Boaz

----- Original Message -----
From: Eleanor Dodson
Date: Thursday, March 19, 2009 11:17
Subject: Re: [ccp4bb] nad woes
To: CCP4BB@JISCMAIL.AC.UK

> Even for NAD I think I would make my own "new" dictionary.
>
> If you go to the ebi site ( now pdbe) ask for Msdchem ( is it
> PDBeChem
> now?)
> Get the idealised NAD coordinates with the remediated nomenclature
> Submit the coordnates to the ProDrg server.
> Retrieve the REFMAC dictionary
>
> Use PDB and dictionary in Coot to fit the ligand..
>
>  Eleanor
>
>
>
>  Get back an idealised dictionary Jan Abendroth wrote:
> > Hi all,
> > is there any wisdom on NAD out there? I experience some
> strange
> > behaviour of this common cofactor.
> >
> > With moderately convincing density, probably low occupancy of
> a
> > cofactor that came along for the ride from E coli,
> Refmac5.5.0088
> > pulls the AN6 atom out of the adenine plane. With my own
> library that
> > puts planar restraints on the adenine ring this seems to be fixed.
> >
> > Coot during real space refinement or regularisation using
> either the
> > standard or my own dictionary handles the purine ring just
> fine,
> > however, totally garbles up the nicotineamide.
> >
> > Btw, I use the * nomenclature.
> >
> > Cheers
> > Jan
> >
> > --
> > Jan Abendroth
> > deCODE biostructures
> > Seattle / Bainbridge Island WA, USA
> > work: JAbendroth_at_decode.is
> > home: Jan.Abendroth_at_gmail.com
> >
> >
>

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd