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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