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
--
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