"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 CaNCCb to +34 deg." p 630 ;-) BR -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Patrick Loll Sent: Monday, April 19, 2010 2:40 PM To: CCP4BB@JISCMAIL.AC.UK 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 pat.l...@drexelmed.edu
