Hi all,
The using of this library
www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
fixes the problem of refmac ! thanks Garib.
Now Coot .... It seems that Coot does not use synonyms. Even so I have
the same library for Refmac and Coot, I'm not abble to manipulate the
DNA in Coot.
Any suggestions ?
Garib Murshudov a écrit :
> It should. At the moment it is dealt with using synonyms. I have only
> done few tests. If it does not solve it then I have done something wrong
> need to correct it.
> If coot uses synonyms then it should be able to deal with these.
> Complete solution of this problem with backward compatablity requires
> multiple naming in cif files and it will take some
> time to sort them out.
>
> Garib
>
> P.S. I have put this dictionary few days ago. It should be in:
> www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
>
>
> On 3 Jan 2008, at 17:33, William Scott wrote:
>
>> 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: [log in to unmask]
>>>> --------------------------------------------------------
>>>>
>>>>
>>>
>>
>>
>
>
--
--------------------------------------------------------
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: [log in to unmask]
--------------------------------------------------------
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