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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>
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--
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
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D-82152 Martinsried
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www.tomotronic.org