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Automated Protein Structure Solution with BnP. Charles M. Weeks¹, Stephen A. Potter¹, Russ Miller^1,2 & William Furey³, ¹Hauptman-Woodward Medical Research Institute & Dept. of Structural Biology, SUNY at Buffalo, 73 High St., Buffalo, NY 14203, ²Center for Computational Research, Norton Hall Rm. 9, SUNY at Buffalo, Buffalo, NY 14260,³Biocrystallography Laboratory, VA Medical Center, University Dr, C, Pittsburgh, PA 15240 and Dept. of Pharmacology, Univ. of Pittsburgh, Pittsburgh, PA 15261.

BnP is a common graphical user interface for the direct-methods program SnB and the protein-phasing package PHASES. Thus, it provides a convenient pathway from intensity data to interpretable protein map. In automatic mode, the user needs only to specify a few parameters, and the entire phasing process from substructure determination through phase refinement and solvent flattening is chained together and started by clicking a single button. On the other hand, a manual mode is available for difficult cases and allows the user to control many parameters and execute the major steps in the phasing process sequentially.

Automated operation is made possible by fine tuning the criteria for recognizing when a substructure solution has occurred, the development of procedures for validating correct heavy-atom sites, and methods for determining whether or not the substructure determined by SnB has the proper hand. Incorrect sites are recognized by an efficient occupancy refinement procedure that successfully eliminates spurious sites even if they are a significant fraction of the total. The PHASES subprogram BNDRY is used to locate the protein/solvent boundary for both enantiomorphs, and the correct hand corresponds to the map with the higher ratio of the standard deviations of the electron density in the protein and solvent regions. Finally, the PHASES subprogram PHASIT is used to implement a standard substructure/phase refinement protocol that is then followed by solvent flattening. In recent tests with three-wavelength MAD data, the substructure and proper hand could be determined in an hour for a series of protein structures ranging in size from 16 to 66 sites, and the full substructure refinement and protein phasing required, at most, an overnight run on a relatively slow 300 mHz SGI R12000 processor. The quality of density maps resulting from various refinement schemes will be compared. BnP is available for download from (http://www.hwi.buffalo.edu/BnP/).