Berhard, Then you have to define what you mean by "smallest". SHELXL uses the (ASCII) alphabetical order of the three atom names for this purpose (SHELX manual page 7-23) so that it is unambiguous (since the names are not allowed to be the same), but presumably other programs use other conventions (e.g. the Cahn-Ingold-Prelog rules).
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 19 Apr 2010, Bernhard Rupp wrote: > "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 >
