Re: [ccp4bb] Protein DNA complex refinement

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

Previous message:
Subject: Re: Protein DNA complex refinement
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-03

Next message:
Subject: Re: Protein DNA complex refinement
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-03

Subject: Re: Protein DNA complex refinement
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-01-03

Also, the PDB now uses prime (') instead of asterisk (*) for the ribose
numberings, and uses OP1 instead of O1P, and so forth.

Do the new refmac dictionaries have that (I haven't been able to get it to
work in the context of coot).

Garib Murshudov wrote:
> If you take new dictionary with new refmac it may solve this and some
> other naming problems.
>
> Try from the website:
>
> www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
>
> Garib
>
> On 3 Jan 2008, at 16:53, Daouda TRAORE wrote:
>
>> Hi all,
>> I'm trying to refine a protein DNA complex using Refmac.
>> Unfortunately the job fails because of the definition of nucleosides :
>> In the pdb file I use for molecular replacement (and it's the same
>> for all protein-DNA complex I found in the PDB) nucleosides are
>> labelled DG, DT, DA , DC. In the monomer libraries for Refmac these
>> are labelled GD, TD, AD, CD.
>> The jobs fails also if I replace the "DG, DT, DA , DC" by "GD, TD,
>> AD, CD" in the coordinate file prior to refinement.
>> Could someone help me.
>>
>> --
>> --------------------------------------------------------
>> Daouda A.K. TRAORE, PhD Student
>>
>> Laboratoire de Cristallographie et Cristallogenèse des Protéines
>> Institut de Biologie Structurale de Grenoble
>> 41 rue Jules Horowitz
>> 38027 Grenoble Cedex 1 - France
>> Phone: @IBS: +33 4 38 78 95 96 @ESRF/FIP: +33 4 76 88 27 89
>> Fax: +33 4 38 78 51 22
>>
>> ************************
>>
>> Laboratoire Chimie et Biologie des Metaux
>> CEA Grenoble iRTSV / LCBM / PMB
>> 17 Avenue des Martyrs
>> 38054 Grenoble Cedex 9 - France
>> Phone : +33 4 38 78 38 75
>> Fax : +33 4 38 78 34 62
>>
>> E-mail: daouda.traore@ibs.fr
>> --------------------------------------------------------
>>
>>
>

CCP4bb navigation

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

Previous message:
Subject: Re: Protein DNA complex refinement
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-03

Next message:
Subject: Re: Protein DNA complex refinement
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-03