RE: cyclic structures

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>
>From: "Frances Bernstein" <bernstei@fcb.pdb.bnl.gov>
>Subject: cyclic structures
>
>     I do not see any discussion of how to present a cyclic polypeptide or
>polynucleotide (should one be synthesized someday) in the mmCIF dictionary.
>The area that this affects in terms of representation is _entity_poly_seq.
>which presents the sequence as linear.
>
>                              Frances C. Bernstein
>

	   I also do not see how the current mmCIF could handle cyclic
	topologies.   However, the proposal I made a the week before
	last would handle these situations quite easily.  Once you
	begin to explicitly list the links between the residues any
	topology can be described -- linear, branched, or cyclic.

	   An example of a cyclic peptide would be (remember this is not
	approved mmCIF).

	loop_
		_entity_link.entity_id
		_entity_link.mon_1_id
		_entity_link.mon_1_id
		_entity_link.link_typ
		_entity_link.primary
	B	1	2	peptide	yes
	B	2	3	peptide	yes
	B	3	4	peptide	yes
	B	4	5	peptide	yes
	B	5	6	peptide	yes
	B	6	1	peptide	yes

	This loop describes a six residue cyclic peptide.  Residue 6 is
	linked back to 1.  One could easily connect this via a disulfide
	bond to another polypeptide to construct something really interesting.

								Dale Tronrud

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