Re: [ccp4bb] chiral volumes--2nd try

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: chiral volumes--2nd try
From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2010-04-19

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Subject: Re: Calculation of electron density map for a twinned dataset
From: Jon Schuermann schuerjp {- at -} ANL {- dot -} GOV
Date: 2010-04-19

Subject: Re: chiral volumes--2nd try
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2010-04-19

"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:CCP4BB@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.loll@drexelmed.edu

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: chiral volumes--2nd try
From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2010-04-19

Next message:
Subject: Re: Calculation of electron density map for a twinned dataset
From: Jon Schuermann schuerjp {- at -} ANL {- dot -} GOV
Date: 2010-04-19