Dear Brian,

If you have time we could do with a little modeling advice.

The problem is still how to set up the MolSystem and the Molecule. We want
a situation where you can have precisely defined but different protonation
state, disulfide bond state, and in general linking for Molecule and
MolSystem. We want to be able to change protonation state and linking, for
MolSystems (not so sure about Molecules), and we want to get the correct
ChemComp for the protonation state etc. any time we inquire for either
Molecule and MolSystem. Then there is your requirement that it must be
possible to make up a MolSystem.Chain as the sum of several Molecules.

We could do it essentially by moving the necessary information into the
MolSystem.Chain, to some extent duplicating the information in the
Molecule. Carried to the extreme all information in Molecule would be
duplicated in MolSystem, which would leave MolSystem as a richer
alternative to Molecule for use by Structural people. In this scenario
there would be essentially no link between Molecule and MolSystem. That is
not ideal.

More cautiously one could have a many-to-many link between Molecule and
MolSystem.Chain and retain the link between MolSystem.Residue and
MolResidue. This would also allow reusing the information about
interresidue linkages in the Molecule package rather than duplicating it
in the MolSystem package. The problem with this is that it is hard to see
what information from the Molecule is still valid in the MolSystem, or, in
other words, what the rules would be for combining Molecules into a single
Chain. What would be the relationship between the Molecule and Chain
sequence, for Polymers? Would you have to use *all* residues in the
molecules you use? In the same order? With all the linkages preserved?
Could you have a Chain consisting of one Molecule with a break, or with
 another Molecule inserted in the middle? What would the significance be
of two organic chemistry Molecules combined in a single Chain? Would
Chains have to be chemically connected? Unless there were some rules a
Chain could be made up from one residue from each of a hundred different
Molecules, and no one would know what it was supposed to mean.

Sorry it got so wordy - a torrent of words is a sign of inner confusion,
certainly in this case. Any help you can give on what you would and would
not want to do with tehse Chains would be appreciated.

Yours,

Rasmus

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Dr. Rasmus H. Fogh                  Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX (01223)766002