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Re: [ccp4bb]: how to align two 2-fold axis?

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If your monomers in the two dimers pack exactly in the same way, you can

superimpose the two dimers and the two-fold axises on the two dimers
fit each other perfectly.

If your monomers in the two dimers does not pack in the same way, it is
easy to fit the two axis together. This change packing can be described
by a
domain movement and there is a Web server DOMOV
http://bioinfo1.mbfys.lu.se/cgi-bin/Domov/domov.cgi   which can help you
detect how much the movement is.  If there is not much change, you can
fit the axises if you superimpose the two dimers. Otherwsie, you can use

coordinates of two points on  the axis (same distance from the
mid-points of
the axis) and the center of two monomers to superimpose these two axis.

If  you use the FIT program (
) to do the superimposition, you can  display the dimer axis by the O

best regards


> > I am making a figure, in which there is a pseudo 2-fold related
> > and another perfect 2-fold related dimer. These two dimer should be
> > connected by some linker.  I am trying to model these two dimers
> > together. the problem is I can never get the two 2-fold axis exactly

> > aligned. I think O is not enough to get it 100% right. So any
> > about how to do that?  If I can get the axis for the pseudo 2-fold
> > then align it with the perfect two-fold (which is already known.),
> > how?
> >

Guoguang Lu, PhD, Universitetslektor
Dept of Molecular Biophysics
Center for Chemistry and Chemical Engineering
Lund University
Box 124, SE-221 00 Lund, Sweden
Phone: (int+46)-46-222 0851; Fax: (int+46)-46-222 4692
e-mail: Guoguang.Lu@mbfys.lu.se  Mobil: 070-777 4029
homepage: http://bioinfo1.mbfys.lu.se