Re: multiple NMR models

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Frances C. Bernstein writes
>
>     The PDB has quite a number of entries whose coordinates
>were derived using NMR.  The most common situation is that the
>depositor provides some number of models plus the minimized
>average structure derived from those models.  The PDB felt that
>it was most appropriate to create one entry for the average
>structure and to keep the multiple models together in another
>entry.  This allows the user to view the multiple models
>readily.  In order to allow the user to separate the models,
>the PDB created the following structure for the multiple model
>entries:
>
>       header material
>       MODEL        1
>       coordinates for model 1
>       ENDMDL
>       MODEL        2
>       coordinates for model 2
>       ENDMDL
>       ...
>       CONECT
>       MASTER
>       END
>
>Note that the PDB numbers the atoms sequentially through the
>entire entry; i.e. atom numbering does not restart with 1
>for each model.
>
>     It would be most helpful if there were a way to handle
>this in mmCIF.

I feel rather strongly that the correct way to
handle this situation is to have separate model
numbers, but the same atoms must have the same
id in each model -- otherwise it is too
difficult to do calculations on the ensemble of
models.

The problem of mapping the mmCIF identification
scheme back into the PDB scheme is something
that has to be dealt with by the PDB, but once
the mmCIF scheme is defined it is properly an
"exercise for the reader" -- in this case the
PDB.

Lynn Ten Eyck

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