scale

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• Previous message: Paula Fitzgerald: "Re: DATABASE_PDB_MATRIX"

     There appears to some confusion about the meaning of SCALE as stored
in PDB entries.

     In the deposition form we ask for all transformations in terms of the
coordinates being submitted to us.  By experience we have found that
generally people have this information for the same coordinate frame in
which they have been working.

     ALL transformations stored in an entry operate on the orthogonal
Angstrom coordinates stored in the entry.  Thus ORIGX in the entry will
transform the coordinates in the entry back to the deposited coordinates
(i.e. it is the inverse of the transformation provided by the depositor).
SCALE in the entry will transform the orthogonal Angstrom coordinates in
the entry to fractional and, as far as I can tell, is identical in
meaning to the mmCIF items _atom_sites.frac_transf_matrix.  MTRIX
transformations are related to non-crystallographic symmetry (and there
can be a number of these in a given entry) and these also operate on the
coordinates stored in the entry.

     Please consult our format description (not the deposition form) for
further information about ORIGX, SCALE, and MTRIX.

     I hope that this clarifies the discussion.

                                 Frances Bernstein

• Previous message: Paula Fitzgerald: "Re: DATABASE_PDB_MATRIX"