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

[Guoguang.Lu@mbfys.lu.se]

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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
should
fit each other perfectly.

If your monomers in the two dimers does not pack in the same way, it is
not
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
to
detect how much the movement is.  If there is not much change, you can
still
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 (
http://bioinfo1.mbfys.lu.se/~guoguang/fit.html
) to do the superimposition, you can  display the dimer axis by the O
program.

best regards

Guoguang


>
> > I am making a figure, in which there is a pseudo 2-fold related
dimer
> > 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
suggestion
> > about how to do that?  If I can get the axis for the pseudo 2-fold
and
> > then align it with the perfect two-fold (which is already known.),
but
> > how?
> >



--
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Guoguang Lu, PhD, Universitetslektor
Dept of Molecular Biophysics
Center for Chemistry and Chemical Engineering
Lund University
Box 124, SE-221 00 Lund, Sweden
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