> This is just basic physics - most restraints are extensive, in that > they > scale with the system size (e.g. excluded volume, stereochemistry). > Any > CC-like restraint is intensive, and doesn't scale with system size. I wouldn't say it has anything to do with physics, but yes, it is obvious once you look at it :-)
> Obviously that doesn't work when you combine the two. The challenge is either making sure people pay attention to to the issue early on or making it go away as a problem so IMP developers don't have to help them individually :-)
> For EM we solved this years ago with a scaling factor. Ideally the > scale > would simply be N^2 where N is the number of particles in the system. Why quadratic rather than linear?
> I don't much like the idea of scaling "regular" restraints by the > number > of atoms or similar, since that would break pretty much everything > else > where the assumption is made that the sum of the restraints is a score > that can be safely minimized I don't see that being able to minimize the score cares about whether it increases as you add atoms - for most cases the number number of atoms is constant or otherwise not interesting (ie if you are docking proteins you don't want a larger protein to automatically score worse) - and if you care about minimizing the number of atoms, you can always add that as a term in your scoring function
> (this assumes that the score does increase > as you add atoms, and restraints on multiple atoms should have more > weight than those on just pairs). Currently the weight scales with the number of particles rather than the number of atoms. The convention I proposed would make it scale with the number of atoms.
A key invariant is that changing the resolution of the representation should not change things too much.