From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
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 (http://alpha2.bmc.uu.se/usf/moleman2_man.html) but I
suppose that this is not the most obvious choice].
Nicholas
--
Dr Nicholas M. Glykos, Department of Molecular
Biology and Genetics, Democritus University of Thrace,
University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
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