Even for NAD I think I would make my own "new" dictionary.
If you go to the ebi site ( now pdbe) ask for Msdchem ( is it PDBeChem
now?)
Get the idealised NAD coordinates with the remediated nomenclature
Submit the coordnates to the ProDrg server.
Retrieve the REFMAC dictionary
Use PDB and dictionary in Coot to fit the ligand..
Eleanor
Get back an idealised dictionary Jan Abendroth wrote:
Hi all,
is there any wisdom on NAD out there? I experience some strange
behaviour of this common cofactor.
With moderately convincing density, probably low occupancy of a
cofactor that came along for the ride from E coli, Refmac5.5.0088
pulls the AN6 atom out of the adenine plane. With my own library that
puts planar restraints on the adenine ring this seems to be fixed.
Coot during real space refinement or regularisation using either the
standard or my own dictionary handles the purine ring just fine,
however, totally garbles up the nicotineamide.
Btw, I use the * nomenclature.
Cheers
Jan
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com
