choice of coordinate frame

Frances Bernstein (bernstei@fcb.pdb.bnl.gov)
Thu, 12 Oct 1995 15:32:55 -0400


     There has been some discussion about coordinate frames
in relation to PDB SCALE transformations.  I would like to
emphasize the importance of presenting coordinates in the
orthogonal frame chosen by the depositor, which may not
necessarily be the default orthogonal coordinate frame.

     There does not appear to be anything in the mmCIF dictionary
that requires that the default frame be used.  In discussing
residue numbering, the dictionary says:

        In all cases, the scheme used here must match the scheme
        used in the publication that describes the structure.

By analogy, one should allow the coordinates to be in the same
frame as used in the publication.  It is not uncommon for a
publication to have discussion of symmetry, present transformations,
etc. all based on a particular (not necessarily default) choice of
coordinate frame.

     In addition, PDB entries carry information in REMARK and other
records that is directly related to the choice of coordinate frame;
it would be impossible to convert automatically and correctly between
PDB and mmCIF if it were mandatory that the coordinates be transformed
into the default coordinate frame when presented in mmCIF.

                                    Frances C. Bernstein