[ccp4bb]: Difficulties with refmac5 dictionary usage: Problem #4

[Ethan Merritt <merritt@u.washington.edu>]

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and yet another....

This one is in the category of a feature request, although if someone can
suggest a way to work around it in the current version I'd be grateful.

I have a sugar which is present as an anomeric mixture of the alpha- and
beta- anomer forms.  How do I describe this to refmac5? 

I have tried two approaches:

1) Remove the chiral volume restraint for the anomeric carbon from the 
dictionary description, and then split the residue into two
partial-occupancy copies with the same residue number but different
ALTLOC flags in the pdb file.  This works, but removing the chiral volume
restraint causes the sugar ring to become distorted during refinement.
What I would like is a new chiral volume keyword that restrains to the
input chirality.  This would also allow to handle prochiral atoms
(e.g. an SP3 Nitrogen with three bonding partners and a lone pair)  
So the choices in the dictionary would be something like
	positiv / negativ / either / prochiral

I had hoped that setting torsion restraints would help keep the ring
conformation stable, but as I reported in my previous post the torsion
restraints are being ignored.

2) Use two dictionary entries, one for the alpha anomer and another
for the beta anomer.  This means that I cannot use ALTLOC identifiers
because the residue codes are now different.  Instead I give two 
different residue numbers but again specify partial occupancy.
Despite the partial occupancies, refmac5 complains treats all the
sugar atoms as close contacts and then segfaults on floating point
errors during the first few seconds of refinement.

Under what circumstances does refmac5 know that a close contact
between two partial occupancy atoms is to be ignored?

I am about to plunge into the refmac5 code to see if I can work out
how to fix at least the ignored torsion restraint problem, but any 
suggestions that would save my time would be much appreciated!

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002