SHARP/autoSHARP References

Copyright	© 2001-2009 by Global Phasing Limited
	All rights reserved.
	This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.
Documentation	(2001-2009)  Clemens Vonrhein
Contact	sharp-develop@GlobalPhasing.com

• J. P. Abrahams and A. G. W. Leslie (1996). Methods used in the structure determination of bovine mitochondrial F₁ ATPase. Acta Cryst. D52, 30-42.
• Agarwal, R. C. (1978). A new least-squares refinement technique based on the fast Fourier transform algorithm. Acta Cryst. A34, 791 - 808.
• Baker, D., Bystroff, C., Fletterick, R. J. & Agard, D. A. PRISM: topologically constrained phased refinement for macromolecular crystallography. (1993). Acta Cryst. D49, 429-439.
• Biou, V., Shu, F. & Ramakrishnan, V. (1995). X-ray crystallography shows that translational initiation factor IF3 consists of two compact a/b domains linked by an a-helix. EMBO J. 14, 4056-4064.
• Blow, D.M. and Crick, F.H.C. (1959) The Treatment of Errors in the Isomorphous Replacement Method. Acta Cryst. 12, 794-802.
• Bricogne G, Vonrhein C, Flensburg C, Schiltz M & Paciorek W. (2003). Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Cryst. D59, 2023-2030.
• Brünger, A. T. (1992). The Free R value: a Novel Statistical Quantity for Assessing the Accuracy of Crystal Structures. Nature 355, 472-474.
• Bystroff, C., Baker, D., Fletterick, R. J. & Agard, D. A. (1993). PRISM: application to the solution of two protein structures. Acta Cryst. D49, 440-448.
• Collaborative Computational Project, Number 4 (1994). The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50. 760-763.
• Cowtan, K. (1994). dm: An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, p34-38.
• Cowtan, K. D. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Cryst. D52, 43-48.
• Cowtan, K. D. (2006). The Buccaneer software for automated model building.Acta Cryst. D62, 1002-1011.
• Cowtan, K. D. (2010). Recent developments in classical density modification.Acta Cryst. D66, 470-478.
• Dumas, P. (1994). The heavy-atom problem: a statistical analysis. I. A priori determination of best scaling, level of substitution, lack of isomorphism and phasing power. Acta Cryst. A50, 526-537.
• Eagles, P. A. M., Johnson, L. N., Joynson, M. A., McMurray, C. H. & Gutfreund, H. (1969). Subunit Structure of Aldolase: Chemical and Crystallographic Evidence. J. Mol. Biol. 45, 533-544.
• Epp, O., Steigemann, W., Formanek, H. & Huber, R. (1971). Crystallographic evidence for the tetrameric subunit structure of l-aspariginase from Escherichia coli. Eur. J. Biochem. 20, 432-437.
• Fortelle, E. de la & Bricogne, G. (1997). Maximum-Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods. In Methods in Enzymology, Vol. 276. Macromolecular Crystallography Part A. C.W. Carter and R.M. Sweet ed. Academic Press, San Diego, pp. 472-494.
• Fan Hai-fu, Woolfson, M. M. & Yao Jia-xing (1993). New techniques of applying multi-wavelength anomalous scattering data. Proc. Roy. Soc. A442, 13-32.
• Hall, S.R. & Subramanian, V. (1982a). Normalized Structure Factors. II. Estimating a Reliable Value of B. Acta Cryst. A38, 590-598.
• Hall, S.R. & Subramanian, V. (1982b). Normalized Structure Factors. III. Estimation of Errors. Acta Cryst. A38, 598-608.
• Hendrickson, W. A., & Lattman, E. E. (1970). Representation of Phase Probability Distributions for Simplified Combination of Independent Phase Informaton. Acta Cryst. B26, 136-143.
• Howell, L. & Smith, D. (1992). Identification of heavy-atom derivatives by normal probability methods. J. Appl. Cryst. 25, 81-86.
• Jones T. A., Zou J.-Y., Cowan S. W. & Kjeldgaard M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110-119.
• Kantardjieff, K. A. & Rupp, B. (2003). Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Science 12, 1865-1871.
• Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Nat. Acad. Sci. USA 48, 1417-1424.
• Kirillova, O. & Lamzin, V. S. (2004). Application of discriminant analysis for recognition of helical structural motifs in electron density maps. Acta Cryst. D, in press.
• Leslie, A. G. W. (1987). A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang. Acta Cryst. A43, 134-136.
• Lu, G. (1999) FINDNCS: A program to detect non-crystallographic symmetries in protein crystals from heavy atoms sites. J. Appl. Cryst. 32, 365.
• Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
• Main, P. (1990). The use of Sayre's equation with constraints for the direct determination of phases. Acta Cryst. A46, 372-377.
• Matthews, B.W. (1968). The Solvent Content of Protein Crystals. J. Mol. Biol. 33, 491-497.
• Merritt, E. A. X-ray Absorption Edges
• Morris, R. J. & Bricogne, G. (2003). Sheldrick's 1.2 Å rule and beyond. Acta Cryst. D59, 615-617.
• Morris, R. J., Blanc, E. & Bricogne, G. (2004). On the interpretation and use of <|E|(2)>(d*) profiles. Acta Cryst. D60, 227-240.
• Morris, R. J., Zwart, P.H., Cohen, S., Fernandez, F.J., Kakaris, M., Kirillova, O., Vonrhein, C., Perrakis, A. & Lamzin, V.S. (2004). Breaking good resolutions with ARP/wARP. J. Synchr. Rad. 11, 56-59.
• Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53, 240-255 .
• Perrakis, A., Morris, R. & Lamzin, V.S. (1999). Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6, 458-63.
• Read, R. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42, 140-149
• Roberts, A. L. U. & Brünger, A. T. (1995). Phase improvement by cross-validated density modification. Acta Cryst. D51, 990-1002.
• Rossmann, M. G. (1990). The molecular replacement method. Acta Cryst. A46, 73-82.
• Rossmann, M. G. & Blow, D. M. (1961). The refinement of structures partially determined by the isomorphous replacement method. Acta Cryst. 14, 641-647.
• Rossmann, M. G. & Blow, D. M. (1962). The detection of sub-units within the crystallographic asymmetric unit. Acta Cryst. 15, 24-31.
• Sasaki, S (1989). National Laboratory for High Energy Physics, Tsukuba, Japan. KEK Report 88-14, 1-136.
• Sayre, D. (1952). The squaring method: a new method for phase determination. Acta Cryst. 5, 60-65.
• Schneider, T. R. & Sheldrick, G. M. (2002). Substructure solution with SHELXD. Acta Cryst. D58, 1772-1779.
• Schuller D. (1996). MAGICSQUASH: More Versatile Non-crystallographic Averaging with Mulitple Constraints. Acta Cryst. D52 425-434.
• Sheldrick, G. M.. SHELX Home.
• Subramanian, V. & Hall, S.R. (1982). Normalized Structure Factors. I. Choice of Scaling Function. Acta Cryst. A38, 577-590.
• Ten Eyck, L. F. (1973). Crystallographic fast Fourier transforms. Acta Cryst. A29, 183-192.
• Terwilliger, T. C. and Eisenberg, D. (1983). Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions. Acta Cryst. A39, 813-817.
• Vonrhein, C. & Schulz, G. E. (1999). Locating proper non-crystallographic symmetry in low-resolution electron-density maps with the program GETAX. Acta Cryst. D55, 225-229.
• Vonrhein, C., Blanc, E., Roversi, P. & Bricogne, G. (2007). Automated structure solution with autoSHARP. Methods Mol Biol 364, 215-30
• Wang, B. C. (1985). Resolution of Phase Ambiguity in Macromolecular Crystallography. Methods Enzymol. 115, 90-112.
• Wilson, A.J.C. (1942). Determination of Absolute from Relative X-ray Intensity. Nature 150, 151-152.
• Wilson, C. & Agard, D. A. (1993). PRISM: automated crystallographic phase refinement by iterative skeletonization. Acta Cryst. A49, 97-104.
• Yao, J.-X., (1981). On the application of phase relationships to complex structures. XVIII. RANTAN-random MULTAN. Acta. Cryst. A37, 642-644.
• Zhang, K. Y. J. & Main, P. (1990a). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A46, 41-46.
• Zhang, K. Y. J. & Main, P. (1990b). The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Cryst. A46, 377-381.