CCP4 Roadmaps
	MOLECULAR REPLACEMENT

MOLECULAR REPLACEMENT AND PRECEDING DATA ANALYSIS

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.

Auxiliary CCP4 programs used in these 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

Other non-CCP4 programs

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

Further reading

CCP4i Documentation on Molecular Replacement

Molecular Replacement Tutorial (I. Tickle)

CCP4 Program Documentation