_atom_sites.cartn_transf_matrix

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• Previous message: Paula Fitzgerald: "Release of mmcif.1991.10.06"

     In the mmCIF dictionary, _atom_sites.cartn_transf_matrix is
described as the '3x3 matrix and used to transform fractional
coordinates in the ATOM_SITE category to Cartesian coordinates in
the same category and the following example is given:

;
    Example 1 - based on PDB entry 5HVP and/or laboratory records for the
                structure corresponding to PDB entry 5HVP
;
;
    _atom_sites.entry_id                   '5HVP'
    _atom_sites.cartn_transform_axes       'c along z, astar along x, b along
y'
    _atom_sites.cartn_transf_matrix[1][1]  58.39
    _atom_sites.cartn_transf_matrix[1][2]   0.00
    _atom_sites.cartn_transf_matrix[1][3]   0.00
    _atom_sites.cartn_transf_matrix[2][1]   0.00
    _atom_sites.cartn_transf_matrix[2][2]  86.70
    _atom_sites.cartn_transf_matrix[2][3]   0.00
    _atom_sites.cartn_transf_matrix[3][1]   0.00
    _atom_sites.cartn_transf_matrix[3][2]   0.00
    _atom_sites.cartn_transf_matrix[3][3]  46.27
    _atom_sites.cartn_transf_vector[1]      0.00
    _atom_sites.cartn_transf_vector[2]      0.00
    _atom_sites.cartn_transf_vector[3]      0.00

This would seem to imply that the coordinates are given in fractional.
But in the atom_site section, the coordinates are given in an
orthogonal coordinate frame.  My first question is whether this
example is correct.

I then looked at the examples given at Rutgers.  The coordinates also are
orthogonal in each of the four examples.  _atom_sites.frac_transf_matrix
is the transformation that one would expect to find to make fractional
from the orthogonal coordinates in the entry.  _atom_sites.cartn_transf_matrix
is an identity transformation in each of the four examples.  My second
question is why this transformation is an identity transformation in each
of the four examples when it is not an identity transformation in 5HVP.

                                 Frances C. Bernstein

• Previous message: Paula Fitzgerald: "Release of mmcif.1991.10.06"