[phenixbb] measuring the angle between two DNA duplexes

Edward A. Berry BerryE at upstate.edu
Mon Jan 20 14:14:40 PST 2014

Pavel Afonine wrote:
 . .

> The underlying procedure would do the following:
>    - extract two sets of coordinates of atoms corresponding to two provided atom selections;
>    - draw two optimal lines (LS fit) passing through the above sets of coordinates;
>    - compute and report angle between those two lines?

This could be innacurate for very short helices (admittedly not the case one usually would 
be looking for angles), or determining the axis of  a short portion of a curved helix. A 
more accurate way to determine the axis- have a long canonical duplex constructed with its 
axis along Z (0,0,1). Superimpose as many residues of that as required on the duplex being 
tested, using only backbone atoms or even only phosphates. Operate on (0,0,1) with the 
resulting operator (i.e. take the third column of the rotation matrix) and use that as a 
vector parallel to the axis of the duplex being tested.

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