CCP4 v7.0 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
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
- aimless - scale together multiple observations of reflections
- 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
- baverage - averages B over main and side chain atoms
- blend - multi-dataset combination and cluster analysis
- 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
- cmapcut - Prepare MR density search
- combat - produces an MTZ file in multirecord form suitable for input to SCALA.
- comit - Composite omit maps
- 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
- edstats - Calculate electron density statistics
- 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
- nautilus - Statistical Model Building
- 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
- othercell - explore equivalent alternative unit cells
- overlapmap - calculates the average of two maps
- pandda - Multi-dataset crystallographic analysis methods for ligands
- 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-2.5.5 - Molecular Replacement, SAD Phasing, Anisotropy Correction, Cell Content Analysis, Translational NCSand Twin Analysis
- phistats - Analysis of agreement between phase sets, and checking it against weighting factors
- pirate - Statistical Phase Improvement
- pisa - Protein interfaces, surfaces and assemblies
- pltdev - convert Plot84 meta-files to PostScript, Tektronix or HPGL
- pointless - determine Laue group
- polarrfn - fast rotation function that works in polar angles
- privateer - Validation of carbohydrate 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
- 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
- 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
- mtz2sca - Convert CCP4 mtz-files containing anomalous data to Scalepack format
- openastexviewer - Java program for display molecular structures and electron density maps
- p842asc - Read and write plot84 and ascii files
- postref - Post-refinement of reflection data
- prelyscar - Predictor of Lysine Carboxylation
- 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