On Fri, Jul 12, 2013 at 1:08 AM, Stefan Krimmer < krim...@staff.uni-marburg.de> wrote:
> in some of my macromolecular crystal structures with resolutions between > 1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are > detectable which show after assignment of a water molecule to these blobs > and subsequent refinement with Phenix.refine a good-looking 2Fo-Fc > electron density. However, 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 > automatically refined by Phenix.refine (occupancy manually set to a value > below 100% followed by refinement) or manually set to 50% and fixed for > this value (Fix occupancy option in phenix.refine). 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. Which one of the two > options described above is the better one? I would be thankful for any > advice and/or literature about this topic. > When I had to deal with this in the past, I followed this advice (from Thomas Schneider): http://www.embl-hamburg.de/~tschneider/shelxl/shelxl_faq/shelxlfaq.html#Q16 This is especially true at the resolutions you're working with; even with subatomic resolution data I believe that the observation in the FAQ (that refining the occupancies doesn't improve R-factors and may even make them worse) will be true in most cases - and regardless of program used, btw. (I can't remember if I ever tried comparing the outcomes myself, though.) -Nat
