Re: Aligning the distance between two centroids with an axis

From: Nicholas M Glykos (
Date: Fri Jan 30 2009 - 05:08:19 CST

Hi Mert,

> What I would like to do is to align the vector v=c1-c2 with the x axis
> (Could also be y axis or z axis).

If |c1-c2| is long enough, then you can probably get away by just rotating
the whole system (molA+molB) so that its axes of inertia are along the
orthogonal frame. There are several programs that can do the trick for
you [we use moleman2 ( but I
suppose that this is not the most obvious choice].


             Dr Nicholas M. Glykos, Department of Molecular 
         Biology and Genetics, Democritus University of Thrace,
   University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
      Tel ++302551030620 (77620),

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