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Re: SCALE and ORIGX

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Fri, 6 Oct 95 10:17:21 EDT 

Herb has sent a couple of messages about the proposed handling of PDB SCALE
and ORIGX matrices and vectors.  It is easy for me to answer them one at a
time.

Herb Bernstein writes:

> How does the newly proposed DATABASE_PDB_MATRIX handling of SCALE
> differ from _atom_sites.fract_transf_matrix ... and _vector ...?

The definition of SCALE (from the PDB documentation) is:

Define a proceudre for obtaining fractional crystallographic coordinates
x(frac), y(frac), z(frac) from the submitted coordinates x(sub), y(sub),
z(sub).

Since the depositor can (in theory, at least, and in practice in many of the
data sets in the PDB) submit coordinates in any coordinate system imagin-
able, there is not necessarily a correspondence between SCALE and
_atom_sites.fract_trans_matrix.

> Also, would it not be clearer to put the ORIGX information in
> as a sub-category of atom_sites, say, as .PDB etc., etc., since
> in fact it is primarily an atom_sites issue and only secondarily
> (if at all) a database issue.   It is a transform to bring the
> dataset back to a coordinate frame the experimenter thought useful.

The same sort of things is true for ORIGX, which is the transformation from
submitted to orthogonal coordinates.  It is for these reasons that we think
that SCALE and ORIGX are PDB specific matrices, and not (again, necessarily)
ones of general interest.

The general interest matrices, the ones that (by definition) convert
orthogonal to fractional and fractional to orthogonal, are in ATOM_SITES,
where, as Herb rightly points out, such information belongs.  We want to
keep the PDB-specific matrices somewhere else, as they have caused a great
deal of confusion over the years, and we want people to have to work hard
to find them.

This discussion is continued in the next message.

Paula

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