
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:
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 pseudotranslation
 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 selfRotation functions
 ROTMAT
 Interconverts CCP4/MERLOT/Xplor rotation angles
 RSEARCH
 Rfactor and correlation coefficient between F_{calc} and F_{obs}
 STNET
 Generate stereographic net plot for use with POLARRFN
 TFFC
 Translation Function Fourier Coefficients
Other nonCCP4 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
