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Nomenclature: The standard residue library of Cyana 2.0 adheres
to strict IUPAC nomenclature for amino acids. Compared to the standard
libraries of Cyana 1.x and Dyana there are the following changes in atom
nomenclature amino acids:
Backbone amide proton: HN --> H
Glycine alpha protons: HA1/HA2 --> HA2/HA3
The most common forms of the amino acid residues are referred to by the
standard three-letter code, i.e. there are the following changes for
charged residues:
LYS+, ARG+, GLU-, ASP- -->
LYS, ARG, GLU, ASP
The straightforward way to convert data files to the new nomenclature
is by using Cyana itself. The demos include an example script for this
purpose, 'MigrateFromDyanaCyana1.cya'.
If, for some reason it is desirable to continue using the old Cyana 1.x/Dyana nomenclature together with the new library, this is possible
simply by inserting the 'translate dyana' command in the local startup
script (./init.cya).
The old Cyana 1.x/Dyana library is still available and can be loaded
with the 'dyanalib' command, whereas 'cyanalib' will load the standard
library that is based on the widely used geometric parameters of Engh and
Huber (Acta Crystallogr. A47, 392-400, 1991).
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