"The problem of discrete values in restraints can be circumvented by
computing
a corresponding continuous value such as a chiral volume Vc, which is given
by
a scalar triple vector product A • (B x C) originating at the central atom.
With the
smallest ligand pointed toward the observer and clockwise assignment of the
vectors, the sign of the chiral volume is positive, and computes to about
2.5 Å3.

An alternative method of restraining chirality is by restraining the
improper torsion
(or improper dihedral or zeta-value) between Ca–N–C–Cb to +34 deg."

p 630 ;-)

BR

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Patrick Loll
Sent: Monday, April 19, 2010 2:40 PM
To: [log in to unmask]
Subject: [ccp4bb] chiral volumes--2nd try

Sorry, the original post looks garbled (mirroring my internal state,  
no doubt).  I'm trying again, sending as plain text:

Friends,

A question about the definition of chiral volumes:

I'm looking for the definition of the SIGN of a chiral volume. The  
only ccp4 reference I can find (readily) is this:

        http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html

This page gives an algorithm for determining the sign, which I  
paraphrase here:

*  Call the central (chiral) carbon a, and its three non-hydrogen  
substituents b, c, and d.
*  Arrange things so that as you look from b to c to d, your eye is  
moving clockwise.
*  If atom a is below the plane formed by b, c, & d, then the chiral  
volume is positive (otherwise negative)

Clear enough.  However, when I start to apply this rule to basically  
every library I have ever used, I get the opposite result.  Try it,  
for example, with the ALA.cif file distributed with ccp4:

_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
  ALA      chir_01  CA     N      CB     C         negativ

Assigning "a" as the centre atom and atoms "b-d" as numbers 1-3, when  
I apply the rule from the refmac page I get a positive chiral volume,  
not the negative one found in the cif file. Ditto for every other  
example that I have tried.

Am I mis-reading what is meant by "above" and "below"?  I'm assuming  
that if atoms b, c, and d all lie in a vertical plane, and you are  
facing that plane, then "below" means on the far side of that plane  
and "above" means between you and the plane.

When I use the definition V1 * (V2 x V3), where V1 is vector FROM  
chiral atom to 1st substituent (e.g., CA to N in alanine example  
above), V2 = vector from chiral atom to 2nd substituent, etc., then I  
get the expected sign for the chiral volume.

So is the refmac page wrong, or am I falling prey to some roaringly  
obvious stupidity?

Having a rough Monday--starting to question my sanity.

Thanks,

Pat

ps It appears that the term "_chem_comp_chir.volume_sign" is not  
defined in either the core or mmCIF dictionaries. Can this be right?

----------------------------------------------------------------------------
-----------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
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