Re: more about PDB Z value

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• Previous message: Frances Bernstein: "more about PDB Z value"
• In reply to: Frances Bernstein: "more about PDB Z value"

Frances has raised the issue of the PDB Z value
and a place to put it in mmCIF.  Personally I
do not see a lot of use for the quantity -- it
doesn't give the crystallographic multiplicity
of asymmetric units, and for heteropolymers
seems to me to be actively misleading.

_cell.formulat_units_Z is rooted in small
molecule crystallography, as is essentially all
of the chemical_formula material.  It seems to
me that the ENTITY data items were defined
because macromolecular crystalls are not as
well defined chemically as small molecule
crystals, and if we need a placeholder for the
PDB Z value we should put one in.  I don't
think we should revise the definitions in a way
that will make mmCIF less compatible with CIF. 
Would revision of the definition of
_cell.formula_units_Z do this?

Lynn Ten Eyck

For context, Frances Bernstein wrote

>_cell.formula_units_Z is defined as:
>
>;              The number of the formula units in the unit cell as specified
>               by _chemical_formula.structural, _chemical_formula.moiety or
>               _chemical_formula.sum.
>;
>
>But when I look at _chemical_formula I find:
>
>;              Data items in the CHEMICAL_FORMULA category would not, in
>               general, be used in a macromolecular CIF.  See instead the
>               ENTITY data items.
>
>which seems to imply that one should not be using _cell.formula_units_Z
>in mmCIF.
>
>Herbert pointed out that if one were to revise the definition of
>_cell.formula_units_Z, it could be used to hold the PDB Z value.
>Apparently Phil Bourne assumes that _cell.formula_units_Z is meant to
>hold the PDB Z value and he uses it for that purpose in pdb2cif.

• Previous message: Frances Bernstein: "more about PDB Z value"
• In reply to: Frances Bernstein: "more about PDB Z value"