[phenixbb] measuring the angle between two DNA duplexes

Alexandre OURJOUMTSEV sacha at igbmc.fr
Tue Jan 21 01:34:39 PST 2014

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 : phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] De la part de Tim Gruene
Envoyé : mardi 21 janvier 2014 10:25
À : phenixbb at phenix-online.org
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.


More information about the phenixbb mailing list