On Nov 2, 2009, at 6:28 AM, Keren Lasker wrote:
> > On Nov 2, 2009, at 6:10 AM, Daniel Russel wrote: > >>> I think we should separate the discussion for >>> fine coarsening ( up to 5 residues) >>> coarse coarsening ( more than 5 residues). >>> >>> For fine coarsening I think the helper function is fine and most >>> restraints would work well with it. >> I still have the question of why bother keeping consecutive >> residues together? As far as I can tell, it produces uniformly >> worse results than allowing them to be separate. Unless there is >> some advantage, it isn't something that should be there. >> > > This is a way of accelerating the optimization. We can benchmark > your updated excluded volume restraint for example to see how well > it preforms with large assemblies - lets look at it today together - > sounds good ? That isn't the question I have. Clearly fewer particles makes things faster :-) My question is: - We have a function which guarantees that consecutive residues are kept together along the backbone. By providing such a guarantee, it limits the set of simplified structures that it can produce
- The more limited set is worse than a set not constrained by that guarantee under various various conditions and metrics discussed before
- If one has a group of residues that really need to be kept together, it is easy enough to simplify them separately from the other residues.
- As far as I can tell, the limited set is not better under any metrics/conditions that we care about. If this is the case, then we shouldn't have a function which simplifies along the backbone. And if this is not the case, I'm wondering when it is not :-)
So the question is when is it useful to someone to guarantee that consecutive residues are kept together?