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Ethan Merritt wrote:
Because it is not necessary to do so. Storing every H coordinate
generated by the
riding model adds no information to the PDB file that is not already
present in the
parsimonious description provided by the header record:
REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Hopefully that is tongue in cheek. If this is your reasoning, why
build a PDB file at all? It contains no information that isn't
already present in your original diffraction images plus a basic book
on chemical bonding.
The point of building the PDB file is not that it adds information
beyond what is contained in the raw diffraction data and an organic
chemistry textbook. The point is to present that data in an easily
interpreted format. Most non-crystallographer scientists will know
what it means if they see hydrogens connected to carbons when they
pull up a structure. If they see:
REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
they are not going to know what it means, even assuming they know to
look for the REMARK 3 line in the PDB file in the first place. Does
it mean that because the crystallographer was confident enough to use
hydrogens during refinement, all oxygens and nitrogens have been
conclusively assigned in asn and gln side chains? Does it mean that
if you knew the definition of "riding positions" you could deduce the
location of a serine hydroxyl hydrogen, the correct tautomer of a
histidine, or the protonation state of a lysine?
Data has to be provided in a representation suitable for the target
audience, not left in an obscure format just because converting it to
a more easily digested form "adds no information". The target
audience for protein structures should be larger than other protein
crystallographers.
--
Eric Bennett
Assistant Director
Center for Drug Design
University of Minnesota
