CCP4 Roadmaps
REFINEMENT
REFINEMENT
Refinement with REFMAC5 requires reflection data, a set of model coordinates, and
a library defining the restraints for standard groups. If a non-standard group is
encountered (in the REVIEW mode), the user has to build up a set of restraints through
the use of SKETCHER/LIBCHECK.
The plain rectangular boxes represent
tasks as in the
CCP4 Graphical User Interface , the steps to take for refinement.
The ellipsoids represent the input and output to and from the various tasks.
Auxiliary CCP4 programs used in these tasks
ANISOANL
Analyse anisotropic displacement parameters
ICOEFL
Vectorially combined scaling of Fobs (Iobs ) with partial Fc 's
LIBCHECK
Monomer library management program
INTRO_MON_LIB
Introduction to the multi-purpose monomer libraries used by REFMAC
MON_LIB
Multi-purpose monomer libraries used by REFMAC
MAKEDICT
Convert PDB file to TNT or PROTIN dictionaries and PROTIN to PDB
NCSREF
NCS phased refinement; refining molecular replacement solutions when the structure contains NCS models
PROTIN
Prepare restraints file for REFMAC (no longer required in REFMAC version 5)
RDENT
Create dictionary files for RESTRAIN from PDB file
REFMAC5
Version 5.0, REFMAC - Maximum Likelihood refinement with automatic restraint-building
RESTRAIN
Macromolecular refinement
RSTATS
Scale together two sets of F's
SFALL
Structure factor calculation and X-ray refinement using forward and reverse FFT
SKETCHER
Monomer library sketcher, an aid to setting up the restraints library for REFMAC5
TLSANL
Evaluate TLS tensors from RESTRAIN
WATNCS
Pick waters which follow NCS and sort out to NCS asymmetric unit
Other non-CCP4 programs
CNS
Crystallography & NMR System
SHELX-97
Structure solution and refinement in one system
TNT
Macromolecular refinement
Further reading
REFMAC 5.0 at York
CCP4i Documentation on Refinement
CCP4 Program Documentation