RE: TER and MODEL

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>From: yaya@aip.org (herbert_bernstein)
>Subject: TER and MODEL
>
>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.
>

	   I disagree strongly with this suggestion.  The problem I
	see with it is not the implementation suggested by Dr. Bernstein
	but the concept of storing connectivity information in the ATOM
	table.  (I also disagree with the use of TER cards in the PDB
	format.)  The fact that a "dummy" atom with undefined position
	must be created indicates the inappropriateness of storing this
	information in this table.

	   I guess the general form of my comment is that the mmCIF
	format should not seek to encompass a direct transliteration of
	the PDB format.  Quite a number of things in the PDB format
	are done the wrong way.  The TER card is one of them.  If the
	topology of the structure is defined completely the termini of
	the chains become obvious.  There is simply no need to place
	dummy atoms in the ATOM table to mark them.

							Dale Tronrud

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