I can't comment about your other questions but I will weigh in on your refinement question.
I may misunderstand exactly what you mean by "Fcalcs become anisotropic" but by my understanding, the answer is yes. I have taken a model and set of structure factors from the PDB when the model was refined w/o an anisotropic correction but where the structure factors show anisotropic fall-off. (1BNA to be exact.) If you compare the deposited model to the SF's you can calculate the anisotropic correction. If you perform further refinement in the presence of an anisotropic correction you will find that the magnitude of the anisotropy correction becomes larger. The Fobs do not change. The only way this can occur is if the Fcalc from the two models have differing anisotropy themselves, but these models consist only of positions and isotropic B factors! Somehow refinement against an anisotropic set of Fobs, without a correction, will result in a set of Fcalc with anisotropy, but not enough anisotropy to properly fit the data, and whatever it is that the refinement program is doing, it is probably not the right answer. To keep your model from being distorted you need some sort of anisotropy correction in your refinement. Dale Tronrud Ben Spiller wrote: > > I refrained from entering the fray during last month’s discussion of > anisotropic data in refinement, but I wonder if there is any consensus > regarding treatment. > > It seems to me that during refinement scaling to calcs should be > superior to even the very elegant likelihood methods. Another problem > exists in calculating a meaningful Patterson, particularly for molrep > where throwing out reflections is unpopular. A third problem seems to > exist in horrific cases where scaling software will not allow inclusion > of the high res terms. Today’s question seems to be about one of the > latter 2 cases. It’s unclear where Katja is stuck. > > For the refinement case, do others think that Fcalcs become > anisotropic? Or that the liklihood method developed by Read and others > is superior even at late stages? > > Thanks, > > Ben > > On 10/5/09 11:21 AM, "Pavel Afonine" <pafon...@lbl.gov> wrote: > > Hi Katja, > > you may consider trying this: > > http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ > > but PLEASE do not deposit "corrected" data to PDB. > > Also, I would just try to refine the structure and see how it goes > (see if you really need to use the above tool). > > Pavel. > > On 10/5/09 8:21 AM, Katja Schleider wrote: > > > > Hi everybody, > > is there a way to improve crystals that diffract strongly > anisotropic? We got data between 2.5 and 4.0 A and scala says > we should cut these data at 3.9 A. It's such a... I want to > solve this structure! > > > greetings > > Katja > > > > __________________________________________________ > Do You Yahoo!? > Sie sind Spam leid? Yahoo! Mail verfügt über einen > herausragenden Schutz gegen Massenmails. > http://mail.yahoo.com > >
