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Re: Discussion Paper #4



Re: Discussion Paper#4


  There is plenty of very many interesting ideas in David's discussion paper #4 and certainly there was a huge amount of work needed to produce it.

  Somehow or other I was worried that the proposed scheme did not allow for alternate descriptions of the topology of the same structure and that for the disorderd TNT case we ended up with almost duplicating information in the FORMULA_UNIT_ATOM and FORMULA_UNIT_BOND loops for the two molecules and then being forced to map them on to each other in the FU2FU loop. My suggestion is to remove all topology information from the FORMULA group and incorporate it into the MOLECULAR group as the highest (first) level of the topology description. The FORMULA group would be reduced to just the FORMULA_UNIT_ATOM loop and would be an atomic description only of the formula unit. The MOLECULAR_UNIT group remains essentially the same but contains the topology information of the highest level which in David's text is incorporated in the FORMULA unit. In the MAPPING section FU2FU is not needed but FU2MU needs an index to identify each mapping (i.e. each set of atomic mappings) so that a loop containing the molecular information which David put in the FORMULA_UNIT loop can be implemented. It seems to me that these changes allows all of the information that David correctly wishes to capture but in a simplified form. In the disordered TNT example there would be just one MOLECULAR_UNIT of index 1 being one complete TNT molecule. There would be two mappings (each with its own index), mapping this one TNT molecule onto two different set of atoms in the FORMULA unit although these two sets need not be disjoint. These FU2MU mappings each need an index because although the topology of the two molecules may be different they may have different conformations or chirality. 

  I seem to have made a small step in the direction of mmCIF with these suggestions but have definitely retained all the information that David wished to capture. I suspect that these changes also make it easier to work this system in conjunction with a database of molecules and molecular fragments which is the only way that it would be used in practice. It also allows distinct descriptions of the topology of one structure to be captured.

  I thsee things a little differently from David concerning 

>GREG:
> - is it
>possible that a molecule may have a lower symmetry order than the
>site symmetry which it occupies in such cases ?
  For me the answer is definitely yes. La coupe du Roi (a way of cutting an apple into two homochiral halves) is just such a case. A structure containing a molecules which are enantiopure but disordered may well shown up an average disordered 'molecule' which is achiral.


  My sincere apologies for having taken so long to reply.

  I hope my comments are still of some use.

H.


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