[phenixbb] measuring the angle between two DNA duplexes
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.
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
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.
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