[MMTK] Fitting data?
wright at esrf.fr
Tue Mar 23 16:46:17 CET 2004
I've just downloaded and had a quick look at the MMTK package, which
looks very impressive (thanks!). I'm wondering if it would be possible
to use it as a basis for fitting some powder diffraction data from
crystalline protein samples... The idea is to add an energy term
proportional to a chi^2 function which describes the fit to the data. I
think I can (eventually) supply the value of this term, and it's
derivatives with respect to x,y,z co-ordinates of the protein atoms in a
unit cell (which could be transformed into an infinite universe). There
is a slight hitch, that for crystallography the structure is described
with the atoms smeared out by a "thermal factor", but given the poor
quality of powder data this can be just left as a constant and one could
forget the time average versus instantaneous configuration question. The
manual (p13) mentions a developers guide, which I did not manage to find
yet - would someone direct me?
From browsing the source, it looks like it should be possible to get
started with the example MMTK_harmonic_oscillator.c etc, with some bits
and pieces to specify the powder dataset, unit cell, space group etc in
the constructor in the associated .py file? I wanted to contact the list
before diving in, things like unit cell and space group probably already
have proper homes in other parts of the library, but the treatment of
symmetry seems a bit vague so far. Currently we're using a package which
is "state of the art" for fitting powder data, and has been recently
modified to treat proteins. The results are great from the point of view
of fitting the powder data, but make me nervous when I look at the
We would benefit greatly if we could do some cross validation, and would
love to run some simulated annealing procedures where we try to find
good stereochemical configurations which happen to fit our data as well.
Ideally I need some advice from someone who knows more about molecular
dynamics, because my background is mainly limited to powder diffraction.
It would be very interesting to generate a complete unit cell, including
water molecules, to address some questions about low resolution
crystallographic data and "solvent scattering" contributions to low
Any help, advice or hints would be greatly appreciated!
Thanks in advance,
PS: If only you could understand how happy I was to find out that I can
"fix" the stereochemistry of a model by running it through a minimiser
with a little command line script! This is already a great help if I can
cycle models back and forth between the powder software and a better
stereochemical minimiser. Until today there was a lot of mouse clicking
needed to accomplish the same thing...
Dr. Jon Wright
European Synchrotron Radiation Facility,
BP-220, F-38043, Grenoble, France
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