Dear all,
I have a question about the chiral volume and a potential error on this
ccp4 website:
https://www.ccp4.ac.uk/html/refmac5/theory/chiral.html
<https://www.ccp4.ac.uk/html/refmac5/theory/chiral.html>
On this website, it is stated:
========================
Procedure to find the sign of a chiral centre¶
<https://www.ccp4.ac.uk/html/refmac5/theory/chiral.html#procedure-to-find-the-sign-of-a-chiral-centre>
1.
Put atom1and draw bonds from the centre (atom1) to atom2, atom3,
atom4as in figure 3. When the eye goes from atom2to atom4it should
travel clockwise.
2.
Assuming that atom2, atom3, atom4are in the plane of the picture,
then if atom1is below the plane, the chiral volume sign is plus, and
otherwise it is minus. If the numbering is based on the sequence
rules, a positive chiral volume corresponds directly to R and
negative to S
========================
The equation to calculate the chiral volume is usually defined as
V = ⅙ (r2-r1) [(r3-r1)x(r4-r1)]
If I do the calculation, I get other results. Here is an example:
X1 0.0 0.0 0.0
X2 0.0 1.0 1.0
X3 1.0 -1.0 1.0
X4 -1.0 -1.0 1.0
Obviously, X1 is below the plane spanned by X2,X3, and X4, and
X2->X3->X4 are arranged clockwise, but the chiral volume calculated by
the equation above is negative (but should be positive according to the
definition above).
Also, L-Alanine has an S configuration, but the chiral volume around
Calpha (N->C(O)->Cbeta) is positive (but should be negative, see above).
Do I do something wrong, or is there a mistake on the CCP4 website?
I would appreciate any help/comment.
Best regards
Matthias
--
========================================
Prof. Dr. G. Matthias Ullmann
Computational Biochemistry
University of Bayreuth
Universitätsstr. 30, NW I
95447 Bayreuth
Germany
Telephone: +49-921-55-3545
e-mail:[email protected]
http://www.bisb.uni-bayreuth.de/
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