Dear Tim and Pavel, It sounds logical to start from a formal geometrical definition WHAT IS a helix axis for ANY helix, in particular a short one (since this looks like the point of discussion). And to address the original question after expressing this formal definition mathematically. Best regards, Sacha Urzhumtsev -----Message d'origine----- De : [email protected] [mailto:[email protected]] De la part de Tim Gruene Envoyé : mardi 21 janvier 2014 10:25 À : [email protected] Objet : Re: [phenixbb] measuring the angle between two DNA duplexes Hi Pavel, that's the method described in http://journals.iucr.org/a/issues/2011/01/00/sc5036/index.html ;-) based on the moments of inertia (a computer scientist might name it differently). I am not sure, though, you would get the desired result for short helices. E.g. a helix defined by three atoms the eigenvalue would point roughly in the direction of the external phosphates, which is far from parallel with the helix axis. Best, Tim