Suggestions for CHEM_LINK and CHEM_COMP Definitions

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• Previous message: Peter Keller: "Re: Status of the review process"

	   I have been looking into the mmCIF means of defining standard
	geometry and trying to understand how the standard geometry
	relates back to the molecule (with mixed success).  So far I
	have developed a few comments on the mmCIF structure.  A more
	philosophical discussion will follow in my next posting.

	1) I think it would be simpler if the data names for atom_id's
	   in chem_link_bond (for example) where the same as those of
	   chem_comp_bond.  In chem_comp_bond the identifier for the
	   first atom in the bond is atom_id_1 but in chem_link_bond
	   it is atom_1_atom_id.  Since the two concepts are the same
	   it seems confusing to have different names.  geom_bond might
	   be considered too.

	2) chem_link has no provision for torsion angles, planes, etc.
	   I would suggest the creation of chem_link_tor, chem_link_chir,
	   chem_link_plane and the associated groups.

	3) There is no provision for pseudorotation angles in either
	   category.  Perhaps chem_comp_pseudor, chem_link_pseudor,
	   and geom_pseudor groups need to be created.

	4) A stereochemical restraint cannot span three monomers.  For
	   example, if you had a group which interposed two atoms between
	   two other groups the torsion angle with comp_id's 1 2 2 3 could
	   not be defined.  I know of no refinement package which will
	   allow this type of restraint but the limitation is in the
	   ability to define such a restraint not in the application of
	   the restraint.  If the mmCIF file could define the restraint
	   a program using a mmCIF standard dictionary could refine it.

	5) There are no examples for chem_link_bond and chem_link_angle.
	   I have created some.  The data are from the Engh & Huber
	   parameters as interpreted by J. P. Priestle.  Obviously these
	   will need to be worked over by someone who knows what they
	   are doing.

_loop
	_chem_link_bond.link_id
	_chem_link_bond.value_angle
	_chem_link_bond.value_angle_esd
	_chem_link_bond.atom_1_atom_id
	_chem_link_bond.atom_1_comp_id
	_chem_link_bond.atom_2_atom_id
	_chem_link_bond.atom_2_comp_id
PEPTIDE	1.458	0.019	N  1 CA 1
PEPTIDE	1.525	0.021	CA 1 C  1
PEPTIDE	1.329	0.014	C  1 N  2
PEPTIDE	1.231	0.020	C  1 O  1

_loop
	_chem_link_angle.link_id
	_chem_link_angle.value_angle
	_chem_link_angle.value_angle_esd
	_chem_link_angle.atom_1_atom_id
	_chem_link_angle.atom_1_comp_id
	_chem_link_angle.atom_2_atom_id
	_chem_link_angle.atom_2_comp_id
	_chem_link_angle.atom_3_atom_id
	_chem_link_angle.atom_3_comp_id
PEPTIDE	111.2	2.8	N  1 CA 1 C  1
PEPTIDE	120.8	1.7	CA 1 C  1 O  1
PEPTIDE	116.2	2.0	CA 1 C  1 N  2
PEPTIDE	123.0	1.6	O  1 C  1 N  2
PEPTIDE	121.7	1.8	C  1 N  2 CA 2

• Previous message: Peter Keller: "Re: Status of the review process"