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 ben@salilab.org 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 > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >