Hi Armando, can be many reasons, a few for instance:
- are you sure the ligand you modeled in is the one that is actually there? - is the positive density around or overlaps with ligand atoms you places? Then that would means ligand parameters are underrefined (need more refinement) or not correctly parameterized. - if that area is totally empty then it could be a flat model bulk-solvent footprint. However, phenix.refine (if you used it) does correct for this unwanted effects automatically. That's all I can tell given the amount of information you provided. If you send files and explain some more I might be able to offer more comments. Pavel On Fri, Jul 18, 2014 at 9:04 AM, Armando Albert <xalb...@iqfr.csic.es> wrote: > Dear all, > I am screening a small library of ligands against my protein crystals. > Following a soaking with different ligands, I collect datasets to 1.9A > resolution and refine them against an empty model without any problem. > What is the meaning of a rather large negative electron density in the > Fo-Fc map at the binding site?. Could it be related to an incorrect bulk > solvent model? > Thank you in advance > Armando
