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Re: scale

Frances Bernstein (bernstei@fcb.pdb.bnl.gov)
Fri, 6 Oct 1995 11:38:19 -0400 

Paula,

     It will create confusion if you have new items for the PDB
SCALE transformation because SCALE maps directly into
_atom_site.frac_transf_matrix.  The definition of ORIGX and SCALE are
unambiguous in the PDB format description and agree with:

          e. The distributed entry will contain:

                1) ORIGX - transformation from the distributed to the
                   submitted coordinates.

                2) SCALE - transformation from the distributed to the
                   fractional coordinates.

I can assure you that, apart from actual errors that we may have missed,
the SCALE transformation in every PDB entry transforms the orthogonal
Angstrom coordinates in the entry to fractional.  (Note that for NMR and
theoretical models we use an identity transformation for SCALE.)

     In the mmCIF dictionary I find:

      used to transform Cartesian coordinates in the ATOM_SITE category to
            fractional coordinates in the same category.

     Could you explain to me what I am missing here?

                                    Frances

P.S. We do not require that coordinates be in the default orthogonal frame
for the space group.  The depositor can use whatever coordinate frame is
desired and SCALE in the entry will generate fractional from the coordinates.