RE: TER and MODEL

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• Previous message: Peter Keller: "ITEM_TYPE_LIST (was RE: TER and MODEL)"

I am not certain what "done in the wrong way" means.  Tagging the
atom sites within a residue to highlight the fact that the residue
is terminal sees a useful concept.  When true structural coordinates
may be missing, having dummy atoms with properly marked
non-coordinates again seems a useful concept.  There are many
ways to achieve similar utility, and the world will not end if
nothing is done, but allowing a TER within the list does provide
a perhaps temporary, but at least simple way to achive that utility.
Please note that it is _not_ position dependent (unlike MODEL, which
seems to go against the grain of mmCIF by being position dependent),
since it carries all the information it needs within its record to
be self-placing in context.  Placing it TER last in its chain is
certainly good style, and considerate of human readers of a CIF,
but the same information would be conveyed to a database no matter
where it was placed.

Now to a practical reality -- there are a lot of PDB style entries
in the world.  Everyone gains by providing at least an interim
means of translation from PDB to CIF and from CIF to PDB.  The very
process of coming to grips with such translations helps all of us
to understand where some important representational issues lie.
If the suggested approach to TER is not optimal, then it would seem
wise to consider what practical alternatives exist, and to implement
at least one of them.
   --  H. J. Bernstein

P.S.  Sorry about typos -- I screwed up my terminal type and
can't enter my editor to correct them.

• Previous message: Peter Keller: "ITEM_TYPE_LIST (was RE: TER and MODEL)"