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sequence representation problems

Frances Bernstein (bernstei@fcb.pdb.bnl.gov)
Mon, 23 Oct 1995 17:15:58 -0400 

     I have looked at the mmCIF fields for sequence in the
entity and entity_reference section and do not see a way to
indicate any of the following:

     1. The sequence is purely a guess based on the electron
        density maps.

     2. Only part of the sequence is known and present in a
        sequence database.

     3. Several parts of the sequence are known but not all of
        it; i.e. one has several stretches.

     4. One only knows approximately how many residues comprise
        the macromolecule.

     5. The authors could fit a stretch of backbone through some
        density but do not know which missing residues that
        stretch corresponds to.  The PDB just released an entry
        like this.

     6. For immunoglobulin FAB fragments, each chain will be
        linked to two separate PRI and/or SwissProt entries.
        Thus it will be necessary to be able to link one run of
        residues to one sequence entry and another run of residues
        to another sequence entry.

     7. I am sure that other people will be able to think of other
        related representation problems.


                                   Frances C. Bernstein