Bulk solvent correction
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These papers were influential for the implementation in phenix.refine
- Jiang, J.-S. & Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115. "Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures."
- A. Fokine & A. Urzhumtsev. Acta Cryst. (2002). D58, 1387-1392. "Flat bulk-solvent model: obtaining optimal parameters" 
- P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005). D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling procedure"  (open access)
In addition, the following important papers should be mentioned:
- A.T. Brunger. Nature Protocols 2, 2728-2733 (2007).
- Fenn, Schneiders, and Brunger Acta Cryst. (2010). D66, 1024-1031  This paper presents the theoretical basis for the Babinet treatment and for several recent hybrid mask reatments that get away from describing the solvent region as "flat".
Writing out, from refmac, FC and PHIC that include bulk solvent:
- FC_ALL PHIC_ALL are modules and phases of the structure factors including bulk solvent. Contributors have been scaled with ML method.
- FC_ALL_LS and PHIC_ALL_LS : Contributors have been scaled with LS method.