TER and MODEL

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• Previous message: Paula Fitzgerald: "Re: another typo"

I am having trouble mapping the PDB TER, MODEL and ENDMDL records to
mmCIF.  While TER is not a critical record type, it is very helpful
in seeing the ends of chains in the ATOM list.  One simple solution
would be to add TER to the loop of _item_enumeration.value within the
_atom_site.group_PDB save frame.  The only problem with this solution
is that there are no coordinates to go with the TER.  To be consistent
with the rest of the examples in cifdic.m95, we should fill the
missing coordinate columns with a period, but that means we have to
ensure that "." is a valid "float" _item_type.code.  Fortunately,
"float" does not yet seem to be formally defined in dd1 2.1.0, so I
would suggest choosing a syntax for float which treats "." as an
acceptable "float".  Then TER would be OK.

The result would be that, in addition to ATOM and HETATM records, we
could have TER records in an _atom_site list exactly parallel to
a PDB entry.  It would also be helpful in fitting information into 80
columns if "HETA" were added to the list as an alternative to HETATM.


Now to MODEL.  There are many ways to handle this.  One simple,
consistent way would be to extend the ATOM_SITES_ALT category to
accept loops of ensemble_id and ranges of atom_site_id1, atom_site_id2
(pointers to atom_site.id) with, say, a domain_id as the required
key to distinguish the rows.  This could also be helpful in handling
microheterogeneity, though a lot more structure is needed there.

  -- H. J. Bernstein (yaya@aip.org)

• Previous message: Paula Fitzgerald: "Re: another typo"