I have a couple of questions regarding how to improve the solvent model as applied to solvent-filled cavities inside proteins.
I am currently nearing the end of refinement of a protein structure at 2.8 A resolution. I recently switched Refmac versions, upon doing this I noticed a modest improvement in R factors, but I also notice some new features in the difference maps. These features don't show up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I suspect that the appearance of these features (which are all located in solvent channels within cavities inside the protein) are probably due to some difference in how the bulk solvent contribution has been applied.
I've attached a picture of one such feature showing the difference between Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both using the same model and refinement parameters).
My questions are therefore:
1) has something substantial changed in the bulk solvent treatment between Refmac versions 5.5 and 5.6?
2) How can I go about changing the bulk solvent treatment to better account for solvent contribution inside the protein cavities?
Best wishes, and thanks in advance for all your help,
- Allister Crow