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Re: request for additional token

Lynn Teneyck (teneyckl@SDSC.EDU)
Fri, 27 Oct 95 15:41:03 -0700 

There he goes again, spoiling a good discussion with facts . . .

Herbert Bernstein (yaya@aip.org) writes

>Here, for those who don't have it handy, is the 1992 PDB commentary
>on Z, which shows, I think, how close to the existing mmCIF
>Z value definition it is:
>
>"Confusion over the value to use for Z (number of molecules per cell)
>arises because of different conceptions of the meaning of 'molecule'.
>We have adopted the (crystallographic) convention that Z should equal
>the number of times the same polymeric chain is contained in the cell.
>In case of different numbers of chains per cell this will be explained
>in the REMARK section and Z will denote the number of the more
>populous species per cell."

This is moderately reasonable; I think in the case of, say, a heterotrimer
A2B I would prefer Z=1 instead of Z=2, because it would seem to me that
the "molecule" is A2B.  However, I believe these cases are rare and there is
not much point arguing over them further.

>That being said, it would seem the definition of _cell.formula_units_Z
>would work with the addition of the following:
>
>For macromolecular structures, the value of _cell.formula_units_Z
>is the number of occurances of the entity defined by _entity_poly_seq
>in the cell.  For heterogeneous combinations of polymers for which
>the populations of distinct polymeric entities with a cell differs,
>the value for the most populous ones will be used.

This works, unless there is a holdout for applying a superstructure of NCS
definitions . . .  I think actually the heterogeneous multimeric problems are
covered in the requirement that the biological unit be defined.

Lynn Ten Eyck