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: [EMAIL PROTECTED]
--------------------------------------------------------
--
--------------------------------------------------------
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: [EMAIL PROTECTED]
--------------------------------------------------------
