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Program suite GENMEM

Programs

The program GENMEM is used to generate randomly phase sets, to select ones resulting in Fourier synthesis with desired connectivity properties and to create output list of the selected phase sets.

genmem_e.pdf - manual for GENMEM program in PDF format;
genmem.exe - executable for Windows;
genmem.for - FORTRAN text of the program;
genmem.dat - the example of the control data file ("script") for GENMEM program; the name of this file is fixed in the program.

The program AVERAGE is used to treat the output of GENMEM program. It produces the alignment of the selected phase sets and their averaging. The output of the program is the list of the "best" phases and corresponding figures of merit.

averag_e.pdf - manual for AVERAGE program in PDF format;
average.exe - executable for Windows;
average.for - FORTRAN text of the program;
average.dat - the example of the control data file ("script") for AVERAGE program; the name of this file is fixed in the program.

The program CONAN may be used to perform connectivity analysis for any Fourier synthesis starting from structure factor magnitudes, phases and corresponding weights.

conan.exe - executable for Windows;
conan.for - FORTRAN text of the program;
conan.dat - the example of the control data file ("script") for CONAN program; the name of this file is fixed in the program.

The auxiliary program LEVEL allows to find correspondence between relative and specific volumes, which defines the choice of cut-off level in the connectivity analysis.

level.exe - executable for Windows;
level.for - FORTRAN text of the program;
level.dat - the example of the control data file ("script") for LEVEL program; the name of this file is fixed in the program.

The file fam.itc contains space group information in the format used by GENMEM suite. Any blocks may be added to this file (for non-standard settings e.g.), or deleted if necessary.

Download programs (Version on May 29, 2012)



Previous version of programs

The use of the connectivity based phasing

Lunin, V.Y., Lunina, N.L. & Urzhumtsev, A.G. (2000). "Connectivity properties of high-density regions and ab initio phasing at low resolution". Acta Cryst., A56, 375-382.
Lunina N., Lunin V.Y. & Urzhumtsev A. (2003). "Connectivity-based ab-initio phasing: from low resolution to a secondary structure". Acta Cryst. D59, 1702-1715.
Fokine A., Lunina N., Lunin V. & Urzhumtsev A. (2003). "Connectivity-based ab-initio phasing at different solvent levels" . Acta Cryst. D59, 850-858.
Lunin, V.Y., Lunina, N.L., Ritter, S., Frey, I., Berg, A., Diderichs, K., Podjarny, A.D., Urzhumtsev, A. & Baumstark M.W. (2001). "Low-resolution data analysis for low-density lipoprotein particle". Acta Cryst., D57, 108-121.
A. Fokine A., Morales R., Contreras-Martel C., Carpentier P., Renault F., Rochu D. & Chabriere E. (2003). "Direct phasing at low resolution of a protein copurified with human paraoxonase (PON1)". Acta Cryst. D59, 2083-2087.
Lunin, V.Y., Lunina, N.L., Petrova, T.E., Skovoroda, T.P., Urzhumtsev, A.G. & Podjarny, A.D. (2000). "Low-resolution ab initio phasing: problems and advances". Acta Cryst. D56, 1223-1232.
Lunin V.Y., Lunina N., Podjarny A., Bockmayr A. & Urzhumtsev A. "Ab initio phasing starting from low resolution". Z.Kristallogr. (2002). 217, 668-685.
Urzhumtsev, A.G., Lunina, N.L., Skovoroda, T.P., Podjarny, A.D. & Lunin, V.Y. (2000). "Density constraints and low-resolution phasing". Acta Cryst., D56, 1233-1244.