Re: multiple NMR structures

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• Previous message: Lynn Teneyck: "Re: multiple NMR structures"

We have at least three levels of alternate configurations of models
with which to deal:  atomic level alernate sites, microheterogeneity
at the sequence level, and full alternate models at a structural
entity level.  There may be more levels, but this provides enough
meat to make some of the problems clear.  A single structure may
have all these levels.  The current dictionary handles the lowest
level very nicely with flags for the alternate sites and declarations
of ensembles to show correlated behavior.  I would suggest that
there is a certain simplicity in simply extending the same approach
to the sequence and entity level.  The problem that arises is
then simply a matter of how to apply these flags to the lists of
sites or monomers or entities.  Again, we may look to the current
dictionary for guidance.  The alternate position flags are placed
within the rows of atomic site lists, and certainly we should
permit more columns of alternate sequence and alternate entity
flags to be placed there, which is what would actually happen in
the innards of an efficient database, but there is also a
representational efficiency to using the indirect approach used
in declaration of ensembles and, say, sheets, of having an external
declaration which creates groups by sets or ranges of identifiers
within the site list or monomer list or entity list.  This may
require a little fiddle in a database load to properly untangle
and distribute the information to the proper rows, but it can be
a great courtesy to human readers of a data set, who need a more
confined context for comprehension than does a computer.
  -- H. J. Bernstein

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