Re: [sdpd] Putting a molecule on a symmetry axis in Espoir

[Vincent Favre-Nicolin <vincefn...@users.sourceforge.net>]

	Hi,

> >like to treat it as a rigid group, but keep it on the axis -
> > allowing it to move up and down the axis and also rotate.  Is
> > this possible in Espoir?
>
> No, translations and rotations are produced randomly, not
> along a given axis. But if Espoir has produced a model
> sufficient for starting the structure refinement, the final
> adjustments should preferably be done by the Rietveld
> method. However, possibly other software can do that job ?
> Fox ? I don't know.

   In Fox, you can fix individually the x, y and z coordinates of an 
atom or a Molecule/Polyhedron (for the latter, it is the geometrical 
center which is fixed, not a given atom). So if your axis is parallel 
to a main crystallographic axis, this should work. I've never tried 
it, actually.
   But as Armel said, this should not be necessary, as if this is 
indeed the correct position for the group of atoms, the algorithm 
should find it with sufficient precision to move to the Rietveld 
refinement part.
   Unless what is necessary is to correct the occupancy to take into 
account the special position, which Fox can do automatically even if 
the atom is only 'close' to the axis, without a priori knowledge of 
which atom is on the special position. In Espoir you can specify the 
special position code per atom, iirc.

	Vincent
-- 
Vincent Favre-Nicolin
Université Joseph Fourier & CEA Grenoble (France)
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net


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