Dear Bernhard, You indeed have plenty of space to extend the margin notes on page 631! In the REFMAC monomer library that is also used by PHENIX, the sign of the chiral volume is explicitely defined for each chiral atom by _chem_comp_chir.volume_sign. For the L-aminoacids it is always defined by the order "N CB C" and the word "negative".
When I wrote SHELXL (long before REFMAC and PHENIX) I decided not to use any dictionaries; they often contain typos and I prefer to write stand-alone executables. I did not want the order of the atoms in the input file to influence the sign. So I used the ASCII (alphabetical) order of the atoms, and I defined the sign so that the L-amino-acids would all have positive C-alpha chiral volumes. Note that the Cahn-Ingold-Prelog rules make L-Cysteine R and the other 18 standard L-amino-acids S, which would be confusing. I suspect that the "sequence rules" described in the REFMAC documentation were not actually always used in determining the order of atoms specified in the monomer library. At least for the standard L-amino-acids (including CB of Thr and Ile) the sign is always opposite to that used by SHELXL. Note that the RTAB instuction in SHELXL can be used to print out chiral volumes without specifying the three bonded atoms, they are taken from the connectivity table. Best wishes, 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 Tue, 20 Apr 2010, Bernhard Rupp wrote: > Actually, I have some space left under the figure caption this section refers > to and > will add the way SHELXL does it as another example. The CIPs are in a sidebar. > > Thx, BR > > -----Original Message----- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of George > M. Sheldrick > Sent: Tuesday, April 20, 2010 12:17 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] chiral volumes--2nd try > > > 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 �3. > > > > 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: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 > > > >
