You are desribing the reason many people limit their refinement to lower resolution! I think it is probably universally true that there are multiple conformations for sidechain/water networks at the surface, which we just dont model properly. If you are going to tackle the fine details you need to judge how the nearby side chains are fitted as well as the water. And of course then you can probably also see stuff present in the crystallisation media.
The rewards are a lower R factor, and a better understanding of mobility I guess. Eleanor On 12 July 2013 09:08, Stefan Krimmer <krim...@staff.uni-marburg.de> wrote: > Dear all, > > I have a question concerning the refinement of partly occupied water > molecules: > > 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. > > Thank you for your help! > > Stefan >
