DATABASE_PDB_MATRIX

herbert_bernstein (yaya@aip.org)
Thu, 5 Oct 95 19:42:11 EDT


I guess the worst problem with the DATABASE_PDB_MATRIX category is
that it fails to respect the very elegant category structure of mmCIF,
which is a powerful tool for searches.  The experimenter's PDB submission
coordinate frame (ORIGX), the PDB reported transform from orthogonal
to fractional (SCALE), the non-crystallogtaphic symmetries (MTRIX),
the translations linking domains of a polysacchatides (TVECT) are
not the sorts of things upon which one might search a database for
the fact that it was reported once upon a time in the PDB, but because
each of them helps in understanding the reported structure, and more
usefully belong linked to other structural information using existing
categories, with, perhaps, appropriate subcategories.

The comment about consistency with "older" PDB reported entries is
irrelevant.  If an experimenter feels such information is useful
in explaining a structure, it should be a matter for his scientific
judgment to report it.  If he does not feel it is useful, he should
not report it.  What he needs in the dictionary is what he can
find in the rest of the dictionary:  a scientifically sound,
non-judgmental, clear exposition of what information is conveyed
by items in the category.

  -- H. J. Bernstein

P.S. The submitted coordinate frame may seem like a minor issue, and
often it, but sometimes can provide useful information about what
happened to make some coordinate directions behave differently
than others.