Hi Stefan,
in some of my macromolecular crystal structures with resolutions between 1.1 - 1.4 Å, mainly in the second solvation shell round positive Fo-Fc electron density blobs are detectable which show after assignment of a water molecule to these blob and subsequent refinement with Phenix refine a good-looking calculated 2Fo-Fc electron density (round shape, the 2Fo-Fc map appears at a contour level of σ = 1.0 - 1.4), but there also occurs a small negative Fo-Fc electron density detectable inside the 2Fo-Fc density blob. The negative Fo-Fc electron density disappears if the occupancy of the water molecule is refined by Phenix or manually set lower than 100% occupancy. Therefore, I think these positions are partly occupied by water molecules, but I am not sure how I should handle it/how it is generally handled. I would be thankful for any advice and/or literature about this topic.
currently phenix.refine can add automatically only fully occupied waters (I am not sure it will ever use atomic model for partially occupied waters). If necessary, add partially occupied waters yourself manually. Make sure they have properly set altlocs (alternative location identifiers): non blank (say A and B).
My second question is concerning a density blob in perfect coordination distance to an indolyl group (perfectly located in the middle of the five-ring, with 3.4 Å distance to every of the five carbon atoms of the five-ring). What‘s the best way to find out which ion possibly occupies this position? I tried Na+ and Ca2+, but after refinement big negative Fo-Fc blobs appear in both cases (maybe the ion at this position is only partly occupied?). There is no anomalous signal detectable at this position (data collection wavelength was 0.91841 nm). After the refinement of a water molecule at this position, a positive Fo-Fc election density is still there.
A manual way of doing this is to come up with a list of potential ion-candidates based on your knowledge of chemistry and what may be in crystallization solution, then try placing one by one, refine anisotropic ADP and occupancy. Make sure you do refinement until convergence, which means you may want to run about 10 or more macro-cycles. Finally, choose the one that results in flattest residual map. I guess Nat's suggestion does something similar to this automatically. Pavel