Re: additional tokens needed for NMR coordinates

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• Previous message: Frances Bernstein: "additional tokens needed for NMR coordinates"

Frances Bernstein writes:

>It would be most helpful if someone in the NMR
>community would work with the mmCIF committee to define some mmCIF
>tokens to store these quantities.  I realize that the NMR community
>is working separately on defining a schema for their data but the
>PDB is facing the reality of having to be able to convert all
>coordinate entries (x-ray and NMR alike) to mmCIF.  The provision
>of additional tokens that fit into the _atom_site category seems to
>be the most appropriate way to handle this conversion.  People
>interested in structures will want to have all coordinate entries
>in one schema so that they will need only one program to input the
>coordinates.

I want to make the following comments concerning the construction of an NMR
dictionary compatible with, or to be incorporated into, the mmCIF dictionary.

An IUPAC task group exists that is preparing recommendations for standards in
publishing NMR structure data and the minimum information that should be
submitted to databanks.  The task group is chaired by Prof. Kurt Wuthrich and
includes Prof. John Markley, Head of BioMagResBank (BMRB). Drafts of the
recommendations have been circulating among the task group members and one
draft was released late last year to a larger scientific audience that included
crystallographers.

At BMRB, we are using these recommendations to create data tokens suitable for
incorporation into the mmCIF dictionary and to be used in the data deposition
form for BMRB.  However, the current IUPAC document is a draft!!!  Changes are
made on a weekly basis.  The draft has not been approved by the full committee
nor reviewed in its final form by an extended portion of the NMR community.
 The recommendations will not be final until IUPAC has approved them.

It would not be appropriate to submit a list of tokens to the mmCIF committee
for incorporation and cannonization into mmCIF, at this time.  The impact on
the NMR community's interactions with PDB, NDB, and BMRB of such an action
would have many implications.  Through the IUPAC task group recommendations and
their review, the NMR community must have the opportunity to define how the
data produced are represented. It is important that the NMR data not be
misrepresented (unintentionally of course), because the data must pass through
a crystallographic lense.  While the argument "coordinates are coordinates" has
been suggested, how the data are reported and what types of supporting
information are provided are significant.

I think it is appropriate to begin discussions with the mmCIF committee on how
to incorporate a list of tokens for solution-state NMR studies into the
dictionary.  We have generated a draft list that is going through a final round
of editing.  An initial list of tokens has been distributed to NMR
spectroscopists for review.  The next draft list will be distributed to NMR
spectroscopists, to the mmCIF committee, and to PDB.


Eldon Ulrich

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