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I believe Garib handles a lot of these things through the use of synonyms, see mon_lib_list.html The section data_comp_synonym_atom_list has things like: Ad . C1* 'C1'' Ad . C2* 'C2'' Is that what you wanted? Not sure if it is complete, e.g. not sure if it works for ADP. Martyn On Wed, 2008-10-08 at 10:06 +0100, Phil Evans wrote: > As far as I understand it (not very far), the PDB version 3 format > changes the naming of ribose ring atoms in nucleic acid to the > conventional C1', C2' etc from the version 2 C1* etc > > > The dictionaries supplied with Coot & Refmac have the V2 style names > C1* etc > > eg a/ADP.cif > > data_comp_ADP > # > loop_ > _chem_comp_atom.comp_id > _chem_comp_atom.atom_id > _chem_comp_atom.type_symbol > _chem_comp_atom.type_energy > _chem_comp_atom.partial_charge > _chem_comp_atom.x > _chem_comp_atom.y > _chem_comp_atom.z > ADP O2A O OP -0.500 0.000 0.000 0.000 > ADP PA P P 0.000 1.026 1.100 0.106 > ADP O1A O OP -0.500 1.921 1.136 1.326 > ADP O3A O O2 0.000 2.021 1.042 -1.149 > ADP PB P P 0.000 1.545 0.853 -2.667 > ADP O3B O OP -0.660 2.802 0.361 -3.341 > ADP O2B O OP -0.660 0.421 -0.149 -2.613 > ADP O1B O OP -0.660 1.204 2.233 -3.157 > ADP O5* O O2 0.000 0.378 2.570 0.052 > ADP C5* C CH2 0.000 -0.566 2.955 -0.916 > ADP H5*1 H H 0.000 -1.399 2.252 -0.844 > ADP H5*2 H H 0.000 -0.084 2.847 -1.890 > ADP C4* C CH1 0.000 -1.083 4.370 -0.761 > ADP H4* H H 0.000 -1.632 4.428 0.189 > ADP C3* C CH1 0.000 -2.090 4.668 -1.916 > ... etc > > Should these dictionaries be changed? > > Phil -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: [log in to unmask] * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************