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Re: [ccp4bb] Protein DNA complex refinement |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 03 January 2008Subject: Re: Protein DNA complex refinement From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-01-03 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 >>> -------------------------------------------------------- >>> >>> >> > > CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 03 January 2008 |
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