[ccp4bb]: Chiral centers in refmac: Bug Fix, Bug, and Request

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

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This is another status report on my attempts to get refmac5 to 
refine an anomeric mixture of sugars.  These points all have 
to do with the handling of chiral volume restraints.

#1 (Bug fix)
============

Refmac5 reports the wrong cutoff value for MONItored values.
The following single line patch to lsq_newdic_rest.f 
fixes the error.

3859c3859
<      &      ' ideal >',TORCUT,'Sigma will be monitored'
---
>      &      ' ideal >',CHICUT,'Sigma will be monitored'

#2 (Bug)
========

I specify "both" as a chiral volume restraint in my dictionary.
My intent is to allow the same dictionary entry to describe both anomers.
This is processed correctly if I run refmac5 with MAKE CHECK NONE.  
But if I comment out MAKE CHECK NONE, then the program resets the
chiral restraint to "positiv", although it otherwise accepts my
dictionary.  

#3 (Bug? or at least lack of documented function)
=================================================

The documentation says that the esd values for chiral restraints 
come from the dictionary, but in fact the dictionary files do not 
contain any such values.  
It seems that there should be a cif entry on the order of
	_chem_comp_chir.volume_esd
This would be analogous to the existing tags 
	_chem_comp_bond.value_dist_esd
	_chem_comp_angle.value_angle_esd
	_chem_comp_tor.value_angle_esd
	_chem_comp_plane_atom.dist_esd
but I see no indication that any of the cif handling routines
create or look for such a tag.

Having the option of setting tighter chiral restraints at
certain centers would really help in some of the cases I am
seeing of ill-behaviour during refinement.

I want to be able to have a dictionary entry:
loop_
	_chem_comp_chir.comp_id
	_chem_comp_chir.id
	_chem_comp_chir.atom_id_centre
	_chem_comp_chir.atom_id_1
	_chem_comp_chir.atom_id_2
	_chem_comp_chir.atom_id_3
	_chem_comp_chir.volume_sign
	_chem_comp_chir.volume_esd
 J15      chir_01  C1     O1     C2     O5   both   0.05


#4 (Feature requests)
=====================

It would be nice if the program reported each time that the 
chirality of a chiral center flips.  Such a flip may or may 
not be exactly what you would like to happen, but without 
notification it's hard to notice that it happened at all so 
that you can inspect it.

Really I think there should be a separate flag in addition to
"both".  Right now if you specify "both" it means that you
don't care which chirality is kept during refinement.
(This is used for LEU and VAL residues). But in my case I
_do_ care; whichever chirality is there on entry I want kept.
But still I want the same dictionary entry to describe
both possible anomers.  So how about a tag "anomer" or
"either" or "keep" or anything of that sort. The chirality
would be monitored on entry to the program and the restraint
flag set to +1 or -1 as appropriate so that the existing
chirality is kept.

-- 
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