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CCP4 v4.2.2 Program Documentation

Reference:
Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763

There is a partial list of program references extracted from the individual program documentation.

Changes:
List of the major program changes since the previous release.

This list can also be seen in function grouping.

BASIC

FILE FORMATS

GENERAL

  • alternate_origins - lists of alternate origins for different spacegroups
  • dm_ncs_averaging - dm for ncs averaging
  • dm_skeletonisation - iterative skeletonisation using dm
  • freerunique - convert FreeRflags between CCP4 and other formats
  • harvesting - harvesting data automatically and using datasets
  • reindexing - information about changing indexing regime
  • scalechoose - information about choice of scaling program
  • twinning - dealing with data from twinned crystals
  • tutorial2000 - tutorial material for CCP4 suite including Data Processing, MAD phasing, Molecular Replacement and Refinement

LIBRARY

  • cciflib - Subroutine Library for handling CCIF files
  • ccplib - utility subroutine library
  • diskio - low-level input/output subroutine library
  • fffear fragment library - map interpretation package
  • keyparse - high-level keyword parsing subroutines
  • lib_list - contents of multi-purpose monomer dictionary used by REFMAC
  • libhtml - Subroutine Library for inserting html tags into log files
  • library - low-level C subroutine library
  • maplib - Subroutine Library for CCP4 map file handling
  • modlib - Subroutine Library for mathematical operations
  • mon_lib - description of multi-purpose monomer dictionary used by REFMAC
  • mtzlib - Subroutine Library for Reflection data file handling
  • parser - parser subroutine library
  • rotamer table - rotamer tables used in the `rotamer' program
  • rwbrook - Library Subroutines for handling the co-ordinate working format
  • symlib - Subroutine Library for handling symmetry operations
  • unix.m4 - library routines for system interactions
  • xdl_view - X-windows based toolkit

SUPPORTED

  • astexviewer - Java program for display molecular structures and electron density maps
  • abs - determine the absolute configuration (hand) of the heavy atom substructure
  • absurd - initial processing of intensity files from MADNES
  • acorn - Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure
  • act - analyse coordinates
  • almn - calculates rotation function overlap values using FFT techniques
  • amore - Jorge Navaza's state-of-the-art molecular replacement package
  • anisoanl - analyses of anisotropic displacement parameters
  • areaimol - Analyse solvent accessible areas
  • arp_waters - Automated Refinement Procedure for refining protein structures
  • baverage - averages B over main and side chain atoms
  • beast - Likelihood-based molecular replacement
  • bones2pdb - Make a PDB pseudo-coordinate file from a bones file
  • bplot - Plot temperature factor by residue
  • cad - Collect and sort crystallographic reflection data from several files
  • cavenv - Calculates cavities in macromolecular structures
  • ccp4mapwish - custom wish interpreter required for MapSlicer
  • cif2mtz - Convert an mmCIF reflection file to MTZ format
  • combat - produces an MTZ file in multirecord form suitable for input to SCALA.
  • contact - computes various types of contacts in protein structures
  • coordconv - Interconvert various coordinate formats
  • crossec - interpolate X-ray cross sections and compute anomalous scattering factors
  • detwin - detwins merohedrally twinned data
  • distang - Distances and angles calculation
  • dm - density modification package
  • dmmulti - multi-xtal density modification package
  • dtrek2mtz - converts d*trek scalemerge output into MTZ format
  • dyndom - determine dynamic domains when two conformations are available
  • ecalc - calculate normalised structure amplitudes
  • f2mtz - Convert a formatted reflection file to MTZ format
  • fffear - map interpretation package
  • ffjoin - joining model fragments from FFFEAR
  • fft - fast Fourier transform
  • fhscal - Scaling of isomorphous derivative data using Kraut's method
  • findncs - detect NCS operations automatically from heavy atom sites
  • freerflag - tags each reflection in an MTZ file with a flag for cross-validation
  • fsearch - 6-d molecular replacement (envelope) search
  • gensym - generate sites by symmetry
  • geomcalc - molecular geometry calculations
  • import/edit protein sequence - Import and edit protein sequences
  • getax - real space correlation search
  • hgen - generate hydrogen atom positions for proteins
  • hklplot - plots a precession photo from an HKL data file
  • hklview - displays zones of reciprocal space as pseudo-precession images
  • icoefl - vectorially combined scaling of Fobs (Iobs) with partial Fc's
  • ipdisp - displays images from a variety of (crystallographic) sources
  • libcheck - monomer library management program
  • loggraph - viewer for CCP4 formatted `log' files
  • lsqkab - apply various transformations to coordinate files
  • makedict - converts PDB file to TNT or PROTIN dictionaries and PROTIN to PDB
  • mama2ccp4 - Convert between `mama' and Cambridge/CCP4 map formats
  • map2fs - convert CCP4 map to XtalView fsfour format
  • mapdump - print a dump of sections of a map file
  • mapmask - map/mask extend program
  • maprot - map skewing, interpolating, rotating, averaging and correlation masking program
  • mapsig - print statistics on signal/noise for translation function map
  • mapslicer - interactive section viewer for CCP4 map files
  • maptona4 - Convert binary map file to and from na4 ascii format
  • matthews_coef - Misha Isupov's Jiffy to calculate Matthews coefficient
  • mlphare - maximum likelihood heavy atom refinement and phase calculation
  • molrep - automated program for molecular replacement
  • mosflm - MOSFLM version 6 for processing image plate and CCD data
  • mtz2various - produces reflexion file for MULTAN, SHELX, TNT, X-PLOR/CNS, CIF or other ascii format
  • mtzMADmod - Generate F+/F- or F/D from other for anomalous data
  • mtzdump - dump data from an MTZ reflection data file
  • mtzmnf - Identify missing data entries in an MTZ file and replace with
  • mtztona4 - interconvert MTZ reflection file and ASCII format
  • mtzutils - Reflection data files utility program
  • ncsmask - averaging mask manipulation program
  • npo - Molecule and map plotting
  • oasis - A program for breaking phase ambiguity in OAS or SIR
  • omit - program to calculate omit-maps according to Bhat procedure
  • overlapmap - calculates the average of two maps
  • pdbset - various useful manipulations on coordinate files
  • peakmax - search for peaks in the electron density map
  • phistats - Analysis of agreement between phase sets, and checking it against weighting factors
  • pltdev - convert Plot84 meta-files to PostScript, Tektronix or HPGL
  • polarrfn - fast rotation function which works in polar angles
  • polypose - program for superimposing many multi-domain structures
  • procheck - programs to check the Stereochemical Quality of Protein Structures
  • professs - determination of NCS operators from heavy atoms
  • rantan - Direct Method module for the determination of heavy atom positions
  • rasmol - Molecular Visualisation Program
  • rdent - Create dictionary entries for Restrain from PDB file
  • rebatch - alter batch numbers in an unmerged MTZ file
  • refmac5 - macromolecular refinement program
  • reindex - produces an MTZ file with h k l reindexed and/or the symmetry changed
  • restrain - macromolecular refinement program
  • revise - estimates optimised value of the normalised anomalous scattering using MAD data
  • rfcorr - Analysis of correlations between cross- and self-Rotation functions
  • rotamer - List amino acids whose side chain torsion angles deviate from the Penultimate Rotamer Library
  • rotgen - Program to simulate X-ray diffraction rotation images
  • rotmat - interconverts CCP4/MERLOT/X-PLOR rotation angles
  • rsearch - R-factor and correlation coefficient between Fcalc and Fobs
  • rsps - heavy atom positions from derivative difference Patterson maps
  • rstats - scale together two sets of F's
  • rwcontents - Count atoms by type
  • sapi - heavy atom site location
  • sc - analyse shape complementarity
  • scala - scale together multiple observations of reflections
  • scaleit - derivative to native scaling
  • scalepack2mtz - converts merged scalepack output into MTZ format
  • sfall - Structure factor calculation and X-ray refinement using forward and reverse FFT
  • sfcheck - program for assessing the agreement between the atomic model and X-ray data
  • sftools - reflection data file utility program
  • sigmaa - Improved Fourier coefficients using calculated phases
  • solomon - density modification (phase improvement) by solvent flipping
  • sortmtz - Sort a MTZ reflection data file
  • sortwater - sort waters by the protein chain to which they "belong"
  • stereo - Extract coordinates from stereo diagrams
  • stgrid - Generate plot to measure angular coordinates on a stereographic projection from polarrfn
  • stnet - Generate plot to measure angles between points on a stereographic projection from polarrfn
  • surface - surface accessibility program and for preparing input file to program volume
  • tffc - Translation Function Fourier Coefficients
  • tlsanl - analysis of TLS tensors and derived anisotropic U factors
  • topp - a topological comparison program
  • tracer - Lattice TRAnsformation and CEll Reduction
  • truncate - obtain structure factor amplitudes using Truncate procedure
  • undupl - remove duplicates from Madnes data, after Absurd
  • unique - Generate a unique list of reflections
  • vecref - Vector-space refinement of heavy atom sites in isomorphous derivatives
  • vectors - generates Patterson vectors from atomic coordinates
  • volume - polyhedral volume around selected atoms
  • watertidy - rationalise waters at the end of refinement
  • watncs - Pick waters which follow NCS and sort out to NCS asymmetric unit
  • watpeak - selects peaks from peakmax and puts them close to the respective protein atoms
  • wilson - Wilson plot, absolute scale and temperature factor
  • xdldataman - manipulation, analysis and reformatting of reflection files
  • xdlmapman - manipulation, analysis and reformatting of electron density maps
  • xloggraph - a viewer of specially formatted `log' files
  • xplot84driver - a viewer for Plot84 meta files

UNSUPPORTED

  • angles - bond lengths, bond angles and dihedral angles from coordinate files
  • axissearch - Check short reciprocal lattive vectors- there may be an alternative definition of unit cell
  • compar - comparison of coordinates
  • extend - obsolete, please use MAPMASK
  • havecs - Generate heavy atom vectors
  • mapexchange - convert map between binary and formatted
  • mapreplace - Combine parts of 2 maps
  • p842asc - Read and write plot84 and ascii files
  • postref - Post-refinement of reflection data
  • protin - (not required, use new refmac)
  • refindex - reindex dataset maximising correlation with
  • refmac - (old version, use refmac5)
  • reforigin - apply best origin shift to PDB atom
  • reform - reformatting coordinates
  • rotaprep - produces an MTZ file in multirecord form suitable for input to SCALA.
  • rwdict - obsolete, please use MAKEDICT
  • vecsum - program to deconvolute a Patterson function and solve the structure
  • zeroed - Set parts of map to zero