Hi, > I think that when you say "as if they were independent," you are begging > the question. You could say that refining in higher symmetry treats the > molecules "as if they were the same." Further, it really assumes more to > posit that they are the same.
But we're still talking about crystals, right? The whole reason for trying to crystallise our proteins/DNA/RNA is because we ideally want a perfect arrangement of molecules. So taking as a starting hypotheses the conservative approach that if the data really looks like P21 it probably is P21 seems a good idea to me. To me it is more a case of refining in lower symmetry treats the molecules "as if they were different" when initially we don't have an indication for it (from data processing). Unless we take the fact that P1 will always give us lower merging R-factors and better indexing scores as indication that actually all our crystals are always P1 ... which they well might be, but probably not within our experimental error. > Really the crux I think is weighing what benefits one gets from > treating the data in different ways. If one can know somehow that > the molecules when treated as p1 differ from each other only as a > function of experimental noise, there would be no reason to treat > them as p1. True: but how do you judge that those differences are within or outside of experimental noise? > On the other hand, if somehow a few sidechains became systematically > different between molecules in the p1 cell, it *would* make sense to > refine in p1, no? What if by refining in P1 the parametrisation makes those side-chains different in the first place? A poorly defined Lys side-chain suddenly becomes two significantly different poorly defined side-chain? Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
