Just to add one more vote: can't agree more, Ed. I remember those days working on implementing ultra-high resolution refinement in phenix.refine and repeatedly heard remarks like "hey, I can figure out if ligand's there at 2A a few refinement cycles away from my MR solution, so why bother with 0.75A dataset: cut it off at 1.5-2A and here you go - problem solved!"
Pavel On Thu, Dec 13, 2012 at 11:00 AM, Ed Pozharski <[email protected]>wrote: > On Thu, 2012-12-13 at 17:50 +0000, Theresa Hsu wrote: > > Being a beginner crystallographer, may I ask a basic question? On how > > many occasions does it make a *biological* difference between having a > > structure at 1.42 and 1.6 A? > > And your definition of "biological difference" is exactly what? Every > field of experimental science strives to obtain results of best possible > quality, why should macromolecular crystallography be different? Would > you be satisfied with a report that "binding assays show presence of > binding which perhaps is in submicromolar range but we don't care to > determine actual binding constants"? > > You should also realize that while ccp4bb has evolved over years into a > forum covering topics well beyond computational aspects of > macromolecular crystallography, at its core it still is made of > individuals who value method development. As Black Queen told Alice - > it takes all the running you can do to keep in the same place. > > > I think this question also extends to adding in water molecules just > > to make statistics look good. > > I never understood this attitude. Compared to O/CNS combination on SGIs > (which are all excellent products) refining a model using COOT/REFMAC on > a modern Core i7 machine is a cakewalk. Let's see - one spends from > several months to a year or two going from gene to diffraction data, and > spending a week carefully rebuilding in order to obtain the best most > complete model possible is undue burden? I am not a perfectionist by > any measure, but deliberately not placing water molecules that you can > place because it "does not make biological difference" can hardly be > justified. > > Cheers, > > Ed. > > > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs >
