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Re: DATABASE_PDB_CAVEAT, DATABASE_PDB_REMARK

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Fri, 3 May 96 9:41:54 EDT 

Herb Bernstein writes:

> In the examples in the mmcif dictionary for both DATABASE_PDB_CAVEAT
> and DATABASE_PDB_REMARK, the ...text shown is the entire PDB record
> with record name, continuations flags, etc.  It would be sufficient
> to carry the text fields per se in the examples, and for the CAVEAT
> example, to combine the multiple text fields into one.  The ...id
> field is not necessary for CAVEAT at present, since a single entry
> can only have only one (possibly continued) CAVEAT record, but
> does no harm and makes for a simpler key than the text itself.

What Herb is asking here is that we actually parse these records, so that
the CIF equivalent contains the information content of the record, but not
its syntax.

We had considered doing this long ago, but we had decided that that was
a dangerous path to follow, as the syntax of these records has changed over
time in the PDB format.  It seems safer to swallow the records whole - that
way they would be there in the CIF version of the data block, and conversion
back to PDB format would be assured of regenerating the original record. 

We talked about this again when we met this Wednesday, and we still think
this is the right course to follow, barring a massive swell of public
sentiment to the contrary.

Paula

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