CCP4 v6.2.992 Program Documentation

Reference:
Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments" - M. D. Winn et al. Acta. Cryst. D67 , 235-242 (2011)

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

BASIC

• ccp4 - introduction to the CCP4 Program Suite
• ccp4_installation - Installation of CCP4 suite
• ccp4_interface_installation - Installation of CCP4 Interface
• ccp4i - interface to the CCP4 programs & file display
• patch_ccp4 - automatically patch CCP4 source code files

GENERAL

• alternate_origins - list of alternate origins for enantiomorphic spacegroups
• alternate_origins_allgroups - list of alternate origins for different spacegroups
• ccp4 roadmaps - roadmaps through the stages of structure determination using the CCP4 suite
• cheshire cells - background information on Cheshire Cells and their uses
• 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
• non-centro_origins - lists of alternate origins for non-centrosymetric spacegroups
• pxmaths - Basic Maths for Protein Crystallographers
• reindexing - information about changing indexing regime
• rotationmatrices - on Eulerian angles, polar angles and direction cosines, and orthogonalisation codes
• scalechoose - information about choice of scaling program
• symmetry - overview of symmetry information
• tutorial - tutorial material for CCP4 suite including Data Processing, MAD phasing, Molecular Replacement and Refinement
• twinning - dealing with data from twinned crystals

SUPPORTED

• abs - determine the absolute configuration (hand) of the heavy atom substructure
• acorn - Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure
• act - analyse coordinates
• afro - multivariate substructure factor amplitude estimation for SAD/MAD and SIRAS
• 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
• astexviewer - Java program for display molecular structures and electron density maps
• baverage - averages B over main and side chain atoms
• bones2pdb - Make a PDB pseudo-coordinate file from a bones file
• bp3 - multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
• buccaneer - Statistical Model Building
• bulk - bulk solvent correction for translation search and rigid body refinement steps of AMoRe
• cad - Collect and sort crystallographic reflection data from several files
• cavenv - Visualise cavities in macromolecular structures
• ccp4mapwish - custom wish interpreter required for MapSlicer
• chainsaw - Mutate a pdb file according to an input sequence alignment
• cif2mtz - Convert an mmCIF reflection file to MTZ format
• cif2xml - Conversion of mmCIF files to XML
• clustalw interface - Graphical Interface to the ClustalW Program
• cmakereference - Generate reference structure for pirate/buccaneer
• combat - produces an MTZ file in multirecord form suitable for input to SCALA.
• contact - computes various types of contacts in protein structures
• convert2mtz - CNS to MTZ conversion
• coord_format - fix PDB format and convert to/from other formats
• coordconv - Interconvert various coordinate formats
• cphasematch - Calculate agreement between phase sets
• crank - Automated structure solution for experimental phasing
• cross_validate - Validation of harvest files for deposition
• crossec - interpolate X-ray cross sections and compute anomalous scattering factors
• csymmatch - Use symmetry to match chains
• ctruncate - Intensity to amplitude conversion
• data harvesting manager - Tool for managing Data Harvesting Files
• detwin - detwins merohedrally twinned data
• dimple - Automated difference map calculation
• distang - Distances and angles calculation
• dm - density modification package
• dmmulti - multi-xtal density modification package
• dtrek2mtz - converts d*trek scalemerge output into MTZ format
• dtrek2scala - initial processing of intensity files from D*TREK
• 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
• gcx - support program to generate crank XML and run crank via a script
• gensym - generate sites by symmetry
• geomcalc - molecular geometry calculations
• gesamt - structural alignment
• 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
• hltofom - Convert to/from Hendrickson-Lattman coefficients
• icoefl - vectorially combined scaling of Fobs (Iobs) with partial Fc's
• import/edit protein sequence - Import and edit protein sequences
• 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 7 for processing image plate and CCD data
• mrbump - automated search model generation and automated molecular replacement
• mtz2cif - produce mmCIF structure factor file suitable for deposition
• mtz2various - produces reflexion file for MULTAN, SHELX, TNT, X-PLOR/CNS, pseudo-SCALEPACK, XtalView, mmCIF 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 a Missing Number Flag (MNF)
• mtztona4 - interconvert MTZ reflection file and ASCII format
• mtzutils - Reflection data files utility program
• ncont - computes various types of contacts in protein structures
• 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
• parrot - density modification package
• pdb_extract - RCSB/PDB Programs for extracting harvest information from program log files
• pdb_merge - merge two coordinate files into one
• pdbcur - various useful manipulations on coordinate files
• pdbset - various useful manipulations on coordinate files
• peakmax - search for peaks in the electron density map
• phaser - Maximum Likelihood Phasing
• phistats - Analysis of agreement between phase sets, and checking it against weighting factors
• pirate - Statistical Phase Improvement
• pltdev - convert Plot84 meta-files to PostScript, Tektronix or HPGL
• pointless - determine Laue group
• polarrfn - fast rotation function that works in polar angles
• procheck - programs to check the Stereochemical Quality of Protein Structures
• prodrg - generation of small molecule coordinates
• professs - determination of NCS operators from heavy atoms
• prosmart - Comparison of chains, and restraints generation
• r500 - Checks PDB files for any problems before submission
• rampage - Ramachandran plots
• rantan - Direct Method module for the determination of heavy atom positions
• rapper - conformer modelling and building
• rasmol - Molecular Visualisation Program
• 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
• 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
• 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
• sequins - Statistical Model Building
• seqwt - Calculate molecular weight from sequence
• 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
• sketcher - monomer library sketcher
• 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
• superpose - structural alignment based on secondary structure matching
• surface - surface accessibility program and for preparing input file to program volume
• symconv - Fetch and convert symmetry and spacegroup information
• tffc - Translation Function Fourier Coefficients
• tlsanl - analysis of TLS tensors and derived anisotropic U factors
• tlsextract - extract TLS group description from a PDB file
• topdraw - Sketchpad for protein topology diagrams
• topp - a topological comparison program
• tracer - Lattice TRAnsformation and CEll Reduction
• truncate - obtain structure factor amplitudes using Truncate procedure
• 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
• xia2 - Automated data reduction
• xplot84driver - a viewer for Plot84 meta files

UNSUPPORTED

• angles - bond lengths, bond angles and dihedral angles from coordinate files
• axissearch - Check short reciprocal lattice vectors- there may be an alternative definition of unit cell
• cmapcut -
• comit -
• compar - comparison of coordinates
• extends - Extend Fourier maps and compute standard uncertainty of electron density
• havecs - Generate heavy atom vectors
• helixang - Program to calculate contacts, angles and separations between helices.
• mapexchange - convert map between binary and formatted
• mapreplace - Combine parts of 2 maps
• p842asc - Read and write plot84 and ascii files
• pisa - Protein interfaces, surfaces and assemblies
• postref - Post-refinement of reflection data
• refindex - reindex dataset maximising correlation with reference dataset
• reforigin - apply best origin shift to PDB atom co-ords according to reference file
• vecsum - program to deconvolute a Patterson function and solve the structure
• zeroed - Set parts of map to zero

DEPRECATED

• arp_waters - Automated Refinement Procedure for refining protein structures
• beast - Likelihood-based molecular replacement
• bplot - Plot temperature factor by residue
• ipdisp - displays images from a variety of (crystallographic) sources
• polypose - program for superimposing many multi-domain structures
• rdent - Create dictionary entries for Restrain from PDB file
• restrain - macromolecular refinement program
• rotaprep - produces an MTZ file in multirecord form suitable for input to SCALA.
• rsearch - R-factor and correlation coefficient between Fcalc and Fobs
• 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

LIBRARY

• c libraries - CCP4 C/C++ Software Library
• cciflib - Subroutine Library for handling CCIF files
• ccplib - utility subroutine library
• cmap library - C/C++ Software Library for CCP4 map files
• cmtz library - C/C++ Software Library for MTZ files
• cparser library - C Software Library for CCP4-style parsing
• csym library - C/C++ Software Library for symmetry information
• diffraction image - CCP4 Diffraction Image Handling Library
• diskio - low-level input/output subroutine library
• dna_output - DNA library for XML output from programs
• fffear fragment library - map interpretation package
• harvlib - Subroutine library for writing CIF harvest files
• 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 - Fortran Software Library for Reflection data file handling
• parser - parser subroutine library
• pxxml - Subroutine Library for writing XML
• rotamer table - rotamer tables used in the `rotamer' program
• rwbrook - Library Subroutines for handling the co-ordinate working format
• symlib - Fortran Software Library for handling symmetry operations
• unix.m4 - library routines for system interactions
• xdl_view - X-windows based toolkit

FILE FORMATS

• intro_mon_lib - description of monomer library used in CCP4
• loggraphformat - Loggraph file format for CCP4
• mmcifformat - mmCIF file format as used in CCP4
• mtzformat - MTZ file format for CCP4
• pdbformat - PDB file format for CCP4