Just as a clarification, the point is not to have a be all and end all
solution, it is to provide a more reasonable starting point and make
it clear that there is a scaling issue. In addition, establishing a
convention about how the error scales with the number of atoms means
that the scaling will have to be changed less after modifications to
the representation (local optimization, rather than a global one :-)
The fact that some restraints types (especially ones which are not
near a minimum of the restraint at the minimum of the whole function)
are difficult isn't really relevant IF some restraints are easy. We
can provide functions/guidelines to handle the easy cases serving the
dual purpose of automating what can be automated and providing a
reminder of what cannot. And, what is easy for us, is not necessarily
easy for others. Whether some are easy outside of diameter and
excluded volume is still under contention though :-)
On Jun 8, 2009, at 1:29 PM, Friedrich Foerster wrote:
if you really want to provide a solution making most people happy i'd
suggest learning from x-ray crystallography. there restraints are
commonly scaled by doing a number of optimizations to get an estimate
for the scaling. a similar solution would be greatly appreciated, but
it is considerable amount of work.
i am pretty sure that any default scaling would by far be insufficient
for most cases, not to speak of 80 %. already ben's example with the
homology-based restraints should make it obvious that a generic
scaling factor is probably impossible to derive in a rather heuristic
framework as imp or modeller.
therefore, if you really intend to make a one-fits-all solution i'd
advocate for a serious effort in analogy to established x-ray
protocols. fudge solutions won't buy anything, i predict. e.g., what
about the resolution of em maps. just to name one problem ...
cheers
frido
On Mon, Jun 8, 2009 at 10:10 PM, Ben Webb <> wrote:
Daniel Russel wrote:
Most physics-based scores are interaction energies between pairs of
particles. But not all of course, otherwise this would be a solved
problem already.
Sure, but for what we do (namely, not gravitation), the number of
pairs
scales linearly with the number of atoms rather than quadratically
(since we have terms with finite cutoffs and packing constraints).
That is not true for Modeller-style homology-derived restraints, as
one
example.
Rescaling a physics forcefield is harmless if all you are
interesting in
doing is preserving minima.
Of course, but rescaling different parts of the forcefield by
different
amounts (e.g. bond terms vs. torsions, since the latter act on
twice as
many atoms) will really break things, and that was what I read your
proposal as.
That said, looking like existing physics
force fields is a reasonable criteria. But that requires that the
other
terms scale with the number of atoms too (since all of the force
fields
have finite cutoffs).
Molecular mechanics people have worked with such nonbonded
interactions
in their forcefields for many years: the effects of such cutoffs on
the
energies and dynamics are well understood. I don't think the same
could
be said for a rescaled term. This is why I suggest rescaling terms
such
as EM and SAXS rather than sterics and nonbonds.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle
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Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried
Tel: +49 89 8578 2651
Fax: +49 89 8578 2641
www.tomotronic.org
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