CCP4: Molecular Replacement roadmap

	CCP4 Roadmaps
	MOLECULAR REPLACEMENT

Before attempting structure determination through molecular replacement, it would be wise to analyse the data in various ways:

Cell Content Analysis - determine solvent content from unit cell description and symmetry
Analyse Data for MR - calculate native Patterson to determine potential pseudo-translation
WILSON - temperature factor analysis; usually done as part of TRUNCATE (Convert Is to SFs (& Analyse Data))
Temperature Factor Analysis

The plain rectangular boxes represent tasks as in the CCP4 Graphical User Interface, the steps to take for molecular replacement. Stippled rectangular boxes represent external programs. 'Edit PDB File' is not part of the Molecular Replacement module in the Interface; it is part of the Coordinate Utilities module.

The ellipsoids represent the input and output to and from the various tasks.

ALMN: Calculate rotation function overlap values using FFT techniques
DISTANG: Distances and angles calculation
ECALC: Calculate normalised structure amplitudes
FFT (Patterson): Check native Patterson map for large peaks which indicate pseudo-translation
GETAX: Real space correlation search / NCS translation search
MAPSIG: Print statistics on signal/noise for translation function map
PDBSET: Various useful manipulations on coordinate files
POLARRFN: Fast rotation function which works in polar angles
RFCORR: Analysis of correlations between cross- and self-Rotation functions
ROTMAT: Interconverts CCP4/MERLOT/X-plor rotation angles
RSEARCH: R-factor and correlation coefficient between F_calc and F_obs
STNET: Generate stereographic net plot for use with POLARRFN
TFFC: Translation Function Fourier Coefficients

COMO: Locked rotation and translation functions
CNS: Patterson correlation method in molecular replacement
EPMR: Molecular replacement using genetic algorithms/evolutionary programming; For documentation, check EPMR CCP14 mirror
Queen of Spades: A stochastic approach to molecular replacement