Apologies, I forgot to attach the dummy pdb file I used. Feel free to check.
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 17:50, Jon Cooper <[email protected]> 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 >> >> 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 > > --------------------------------------------------------------- > > 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/
dummyala.pdb
Description: application/aportisdoc
