Thank you for your comment, but I think it has nothing to do with acute
angles. Also when you look at standard aminoacids like L-alanine, you
get the wrong behavior:
L-Alanine has an S configuration (so should have a negative chiral
volume according to the CCP4 website), but the chiral volume around
Calpha (N->C(O)->Cbeta, following the sequence rule) is positive
according to my calculations.
Let's think about the geometrical interpretation of the equation:
The cross product [(r3-r1)x(r4-r1)]generates a vector perpendicular to
the plane spanned by these two vectors (using the right-hand rule), and
the scalar product projects this vector on to (r2-r1). And if you
consider this, I think there is a mistake on the webpage ...
All the best
Matthias
On 12.02.26 18:49, Jon Cooper wrote:
Hello, I get the same result. I believe it is because one of the
angles in your tetrahedron is acute, which would not be the case for a
chemical entity.
Best wishes, *Jon Cooper* (Emeritus at UCL) [email protected]
Erratum and other hopefully useful things: https://crxp.org.uk
Sent with Proton Mail <https://proton.me/mail/home> secure email.
On Thursday, 12 February 2026 at 08:14, Matthias Ullmann
<[email protected]> wrote:
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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