Hi James, As an aside (as your point is looking for a John Henry, not investigating automated model-building) I would point out that it is not uncommon at all to find cases where a very small difference in starting parameters or starting phases leads to a very different final result in automated model-building. I suspect that this comes from the discrete nature of model-building: an atom goes either here or there and every time you put in something you have branched the search...then when this model is used in calculating a map you get a new map that depends on the exact branching...so that small starting perturbations can become amplified.
As you have found a way to automatically build "possible.mtz" I would expect that some small change in parameters or software would solve the impossible one too (not that one could necessarily find this change easily). All the best, Tom T On Jan 11, 2013, at 12:13 PM, James Holton wrote: > I have a challenge for all those expert model-builders out there: can you > beat the machine? > > It seems these days that everything is automated, and the only decision left > for a crystallographer to make is which automation package to use. But has > crystallography really been "solved"? Is looking at maps now no more > interesting than playing chess, or any of the other once noble pursuits of > human beings that we no longer see as "challenging" because someone built a > machine that can do the job better than any of us? > > I think not. But I need your help to prove it. > > Specifically, the phases in this file: > http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz > when fed with the right set of parameters into the best model building > package I have available to me actually does converge to the correct > structure, with nice low R/Rfree. > However, THIS file: > http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz > contains the same amplitudes but very slightly different phases from those in > "possible.mtz" above, and this file invariably leads to abysmal failure of > every model-building package I have tried. > > Short of cheating (aka using molecular replacement with the "right ansswer": > 3dko), I don't think there is any automated way to arrive at a solved > structure from "impossible.mtz". What is interesting about this is how > remarkably similar these two maps are. In fact, the correlation coefficient > between them is 0.92. And yet, one can be solved automatically, and the other > can't. > > More details can be found on the web page: > http://bl831.als.lbl.gov/~jamesh/challenge/ > > But, my question for the CCP4BB is: > > Are there any "John Henry"s left out there who can still "beat the > machine"? Anyone? > > -James Holton > MAD Scientist
