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Re: Suggestions for CHEM_LINK and CHEM_COMP Definitions

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Fri, 6 Oct 95 14:44:52 EDT 

Dale Tronrud write:

> 	   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.

I'm all for consistency, and I changed the CHEM_LINK data items to match the
style of the CHEM_COMP data items.  However, geom is a little trickier, as it
is a categroy we pulled over from the core.  I'm going to have to confer with
my colleagues about this (we failed to notice this little detail the first
time we talked about this.)

> 	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.

These categories have been added.

> 	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.

Here I'm not sure what pseudo rotation angles you would like to have - if you
can be more specific, we can certainly add them.

> 	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.

It is true that we think of these linkages as being between two components
and not three in the way we have set up the formalism.  There is nothing to
stop us from setting up a three-party formalism, though - we might call it
bridge instead of link.  But is this something that we really need?  I'm
always willing to be persuaded.

> 	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

Outstanding of Dale to have provided examples - the only real syntax problem
here is that it should be loop_ instead of _loop.  I have added these to the
dictionary.

Paula

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