Sorry, you are right. I believe there is a typo as shown below. The reason the coordinates you sent have a negative chiral volume is because it is a D-amino acid, at least in the way I assigned the atoms.
Best wishes, Jon Cooper (Emeritus at UCL) [email protected] Erratum and other hopefully useful things: [https://crxp.org.uk](https://crxp.org.uk/) Sent from [Proton Mail](https://proton.me/mail/home) for Android. -------- Original Message -------- On Thursday, 02/12/26 at 18:53 Matthias Ullmann <[email protected]> wrote: > 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](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]>](mailto:[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 >>> >>> 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) >>> >>> - >>> >>> Put atom1 and draw bonds from the centre (atom1) to atom2, atom3, atom4 as >>> in figure 3. When the eye goes from atom2 to atom4 it should travel >>> clockwise. >>> >>> - >>> >>> Assuming that atom2, atom3, atom4 are in the plane of the picture, then if >>> atom1 is 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/ >>> ======================================== >>> >>> --------------------------------------------------------------- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > ======================================== > 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/ > ======================================== > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
