Hi Everyone, I think it's time to review this subject since it is one of the most frequently asked questions. Ironically, I think this is because we tried to make it as clear as possible -:) So, what kind of maps phenix.refine outputs by default? phenix.refine outputs two types of maximum-likelihood weighted maps (or, in other words, sigmaa-weighted maps): 2mFo-DFc and mFo-DFc. Now, as many of you noticed, the MTZ file with map coefficients "_map_coeffs.mtz" contains in fact four maps: 2mFo-DFc and mFo-DFc, and "filled" 2mFo-DFc and mFo-DFc (in fact fo-fc maps should be nearly identical; actually I have to fix it and not write identical fo-fc maps). The first two maps are computed using original Fobs (Fo), and the last two maps are computed using "filled Fobs", that is the original Fobs where missing reflections are "filled" with DFc. It is well known (I can spell a long list or references) that the data incompleteness affects the map quality, and sometimes, certain types of data incompleteness can *severely* distort maps. A possible solution (in order to reduce this negative effect) is to "model" missing Fobs somehow. One possibility is just to put in DFc in place where Fobs is missing, or as suggested by the classics, one can use <Fobs> taken in a resolution bin around a missing reflection. I even tried to use the random numbers and it was also better than doing nothing. Obviously, there is a nearly invisible line between the benefits of "filling in" missing Fobs and introducing bias. Where this line goes - is the subject of a research that to my knowledge is not done yet. Anyway, this is why phenix.refine writes out "regular" and "filled" maps: one is to give you unbiased but eventually lower quality map, and the other one is to give you a better-looking map with a risk of being biased. This way users have more options in exploring their maps (and less reasons for saying that Refmac produces better-appearing maps than phenix.refine -- see below). I have to mention that to my knowledge REFMAC always writes "filled" maps (those with missing Fobs substituted by DFc): - it is mentioned in Maria Turkenburg's thesis: http://www.ysbl.york.ac.uk/~mgwt/thesis-tth/chapter2.html#tth_sEc2.6.5 - and in Refmac docs: http://www.ccp4.ac.uk/html/refmac5/keywords/xray-general.html "Missing Data: For those reflections where the FP are missing, mFo is set equal to dFc. (...)". Correct me if I'm missing something. Please let me know if I wasn't clear in my attempt to explain this. I will update the phenix.refine documentation accordingly. Pavel.