I agree, these changes should fix the problem.
All the best
Matthias
On 14.02.26 23:35, Jon Cooper wrote:
Dear all, having read this part of the refmac documentation a few times:
https://www.ccp4.ac.uk/html/refmac5/theory/chiral.html
I think the following changes are needed to address Matthias's points
and make everything consistent:
https://u.cubeupload.com/jbcooper/refmacdoctweak1.jpg
and further down:
https://u.cubeupload.com/jbcooper/refmacdoctweak2.jpg
These changes affect the text only and preserve the idea of going from
highest priority atom -> mid-priority atom -> lowest priority atom in
a clockwise direction. Hope some of this helps.
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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Prof. Dr. G. Matthias Ullmann
Computational Biochemistry
University of Bayreuth
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