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Re: [ccp4bb] Protein DNA complex refinement |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 04 January 2008Subject: Re: Protein DNA complex refinement From: Daouda TRAORE daouda {- dot -} traore {- at -} IBS {- dot -} FR Date: 2008-01-04 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: daouda.traore@ibs.fr >>>> -------------------------------------------------------- >>>> >>>> >>> >> >> > > -- -------------------------------------------------------- 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 navigationCCP4bb <-- 2008 <-- January 2008 <-- 04 January 2008 |
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