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Re: DATABASE_PDB_MATRIX

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Fri, 6 Oct 95 10:22:39 EDT 

Herb Bernstein writes:

> I guess the worst problem with the DATABASE_PDB_MATRIX category is
> that it fails to respect the very elegant category structure of mmCIF,
> which is a powerful tool for searches.  The experimenter's PDB submission
> coordinate frame (ORIGX), the PDB reported transform from orthogonal
> to fractional (SCALE), the non-crystallogtaphic symmetries (MTRIX),
> the translations linking domains of a polysacchatides (TVECT) are
> not the sorts of things upon which one might search a database for
> the fact that it was reported once upon a time in the PDB, but because
> each of them helps in understanding the reported structure, and more
> usefully belong linked to other structural information using existing
> categories, with, perhaps, appropriate subcategories.
> 
> The comment about consistency with "older" PDB reported entries is
> irrelevant.  If an experimenter feels such information is useful
> in explaining a structure, it should be a matter for his scientific
> judgment to report it.  If he does not feel it is useful, he should
> not report it.  What he needs in the dictionary is what he can
> find in the rest of the dictionary:  a scientifically sound,
> non-judgmental, clear exposition of what information is conveyed
> by items in the category.
>
>   -- H. J. Bernstein
> 
> P.S. The submitted coordinate frame may seem like a minor issue, and
> often it, but sometimes can provide useful information about what
> happened to make some coordinate directions behave differently
> than others.

I've already said why I feel ORIGX and SCALE ought to be somewhere out of the
way.  What I want to add here is a response to Herb's very relevant issue 
that the depositor may feel that there is useful information in representing
the structure in a reference frame other that the crystallographic one.

We agree, and we have provided for that in the STRUCT_VIEW category (I'm
perfectly willing to admit that the details of STRUCT_VIEW may need some
work, but the concept is valid).  This the is place for rotating and
translating the the structure to a view that is meaningful to the structure
(say one with non-crystallographic symmetric aligned with the axes of the
reference frames) and for telling the user what you have done and why.

Paula

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