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Bulk solvent correction: Difference between revisions
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(New page: 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 diffract...) |
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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" [http://dx.doi.org/10.1107/S0907444902010284] | |||
" | |||
* 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" [http://journals.iucr.org/d/issues/2005/07/00/gx5040/index.html] (open access) | |||
bulk-solvent | |||
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 [http://dx.doi.org/10.1107/S0907444910031045] 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. | |||