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Re: Suggestions for CHEM_LINK and CHEM_COMP Definitions

Lynn Teneyck (teneyckl@SDSC.EDU)
Fri, 06 Oct 95 12:15:47 -0700 

Paula Fitzgerald responds to Dale Tronrud:
>Dale Tronrud write:
[snip]
>> 	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.

The canonical example is an iron-sulfur cluster.  The most sensible
view of this entity is ferrocentric, but definition of the bond angles
requires 3-party restraints.  Potentially n-body restraints could
require n-residue specification syntax.

So far these instances are sufficiently uncommon that an escape
mechanism to permit fully qualified atom names MIGHT work, but that
almost defeats the purpose of dictionaries.  If we defer the
dictionary problem we could at least describe what was done with an
"additional restraint" catagory which does break out fully qualified
atom names.

Is this a bigger can of worms than solving the dictionary problem for
defining such restraints?

Lynn Ten Eyck
-----------------------------------
Lynn F. Ten Eyck (teneyck@sdsc.edu)    Tel: (619) 534-8189
San Diego Supercomputer Center         FAX: (619) 534-8193
P.O. Box 85608
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