Chemical structures etc.

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• Previous message: John Westbrook: "Re: mmcif.09.aug.95.. ."

I have a few questions on constructing chemical structures.

1.  How would a mixed polymer of nucleic acids and deoxynucleic acids be
described?  Would one type of monomer be considered standard and the others
given non-standard ids that would then be linked to the standard structures.

2.  Within the ENTITY and CHEM_LINK_BOND sections it does not seem possible to
describe how a non-standard amino acid is linked to adjacent monomers.  For
example how to describe iso-aspartyl group linked through the side-chain
carboxyl to the following amino acid.  I could not find away to get from this
section back to a specific set of two residues in the sequence of a polymer.

3.  Is there a data name for defining a chiral atom as having an R or S
configuration?  I could not find this in the ENTITY or CHEM_COMP sections.


Comment:

The Klyne and Prelog reference given in the GEOM_TORSION group is, I believe, a
bit of misinformation carried over from the core CIF.  As referenced this paper
does not exist and the correct reference is Experientia 16, 521-523 (1960).

Eldon

• Previous message: John Westbrook: "Re: mmcif.09.aug.95.. ."