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multiple NMR models

Frances Bernstein (bernstei@fcb.pdb.bnl.gov)
Fri, 20 Oct 1995 12:48:26 -0400 

     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.

      The most compact way that I thought of would be to create
      new items that could appear in a list that would present
      the model number along with the first and last atom
      numbers (from _atom_site.id) associated with that model.
      But this assumes that _atom_site.id is the sequential
      atom number that appears in a PDB file.

      Alternatively an additional parameter could be defined
      in _atom_site that would present the NMR model number.
      This makes no assumptions about the contents of
      atom_site.id but means that an additional field must be
      present for each atom in a multiple model entry.  In
      general, the PDB uses sequential model numbers starting
      with 1.  But the largest NMR sets currently in the PDB
      contain more than 99999 atoms (current PDB limit given
      our format).  In this case we create several entries.
      The first contains models 1 through N, the second N + 1
      through 2N, etc.

     Because this issue relates directly to the representation of
atomic coordinates, I feel that it would best be handled by the
mmCIF committee.  Thank you.

                                    Frances C. Bernstein