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Re: scale

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Fri, 6 Oct 95 11:04:56 EDT 

Frances Bernstein:

>      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.

OK, I will admit that what I am quoting from is the deposition form.  
It says (March 3, 1995):

--------------------------------------------------------------------------------
ORIGX
        Specify the transformation to convert submitted data to
        orthogonal coordinates to be used in the distributed entry.
        This will be an identity matrix and null vector if the
        submitted coordinates are in an orthonormal (Angstrom units)
        axial system.

[ ] [ ] [ ]   (Xsubmitted)   [ ]   (Xdistributed)
[ ] [ ] [ ] X (Ysubmitted) + [ ] = (Ydistributed)
[ ] [ ] [ ]   (Zsubmitted)   [ ]   (Zdistributed)

--------------------------------------------------------------------------------
SCALE
        Specify the transformation to convert the submitted coordinates
        to a fractional crystallographic axial system.  Note that the
        distributed entry will be in an orthonormal system.

[ ] [ ] [ ]   (Xsubmitted)   [ ]   (Xfractional)
[ ] [ ] [ ] X (Ysubmitted) + [ ] = (Yfractional)
[ ] [ ] [ ]   (Zsubmitted)   [ ]   (Zfractional)

--------------------------------------------------------------------------------
 
i.e., both ORIGX and SCALE operate *ON* the submitted coordinates.

Of course, the same document says:

          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.

Perhaps Fran could quote the Format Description for us, as I don't have that
handy in electron form.  But I think my point that the ORIGX and SCALE
matrices are confusing stands, and I would like the CIF dictionary to carry
unambigous tranformations with unambiguous definitions.  We are providing a
mechanism for keeping the PDB ones, but I'm firm in stating that SCALE is not
uniformly going to correspond to _atom_site.frac_transf_matrix.

Paula

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