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.

AUTOMATED MODEL BUILDING

• privateer - Validation of carbohydrate structures

COORDINATE FILE MANIPULATIONS

• bones2pdb - Make a PDB pseudo-coordinate file from a bones file
• chainsaw - Mutate a pdb file according to an input sequence alignment
• clustalw interface - Graphical Interface to the ClustalW Program
• coordconv - Interconvert various coordinate formats
• coord_format - fix PDB format and convert to/from other formats
• csymmatch - Use symmetry to match chains
• gensym - generate sites by symmetry
• geomcalc - molecular geometry calculations
• gesamt - structural alignment
• hgen - generate hydrogen atom positions for proteins
• lsqkab - apply various transformations to coordinate files
• makedict - converts PDB file to TNT or PROTIN dictionaries and PROTIN to PDB
• pdbcur - various useful manipulations on coordinate files
• pdb_merge - merge two coordinate files into one
• pdbset - various useful manipulations on coordinate files
• reforigin - Apply best origin shift to PDB atom co-ords according to reference file (unsupported)
• rwcontents - Count atoms by type
• sortwater - sort waters by the protein chain to which they "belong"
• superpose - structural alignment based on secondary structure matching
• watertidy - rationalise waters at the end of refinement
• watpeak - selects peaks from peakmax and puts them close to the respective protein atoms

DATA HARVESTING AND DATASETS

• cif2xml - Conversion of mmCIF files to XML
• cross_validate - Validation of harvest files for deposition
• data harvesting manager - Tool for managing Data Harvesting Files
• harvesting - harvesting data automatically and using datasets
• harvlib - Subroutine library for writing CIF harvest files
• pdb_extract - RCSB/PDB Programs for extracting harvest information from program log files
• r500 - Checks PDB files for any problems before submission

DATA PROCESSING AND REDUCTION

• aimless - scale together multiple observations of reflections
• blend - multi-dataset combination and cluster analysis
• combat - produces an MTZ file in multirecord form suitable for input to SCALA.
• crossec - interpolate X-ray cross sections and compute anomalous scattering factors
• ctruncate - Intensity to amplitude conversion
• detwin - detwins merohedrally twinned data
• dtrek2mtz - converts d*trek scalemerge output into MTZ format
• dtrek2scala - initial processing of intensity files from D*TREK
• othercell - explore equivalent alternative unit cells
• pointless - determine Laue group
• rebatch - alter batch numbers in an unmerged MTZ file
• reindex - produces an MTZ file with h k l reindexed and/or the symmetry changed
• reindexing - information about changing indexing regime (see reindex)
• rotaprep - produces an MTZ file in multirecord form suitable for input to SCALA.
• scala - scale together multiple observations of reflections
• scalepack2mtz - converts merged scalepack output into MTZ format
• truncate - obtain structure factor amplitudes using Truncate procedure
• twinning - dealing with data from twinned crystals
• unique - Generate a unique list of reflections (including uniqueify)
• wilson - Wilson plot, absolute scale and temperature factor
• xia2 - Automated data reduction

DENSITY FITTING AND MODEL BUILDING

• arp_waters - Automated Refinement Procedure for refining protein structures
• buccaneer - Statistical Model Building
• prodrg - generation of small molecule coordinates
• fffear fragment library - map interpretation package
• fffear - map interpretation package
• ffjoin - joining model fragments from FFFEAR
• rapper - conformer modelling and building
• sequins - Statistical Model Building

DENSITY MODIFICATION - MOLECULAR AVERAGING

• hltofom - Convert to/from Hendrickson-Lattman coefficients
• cmakereference - Generate reference structure for pirate/buccaneer
• pirate - Statistical Phase Improvement
• dm - density modification package
• dmmulti - multi-xtal density modification package
• dm_ncs_averaging - dm for ncs averaging (see DM program)
• dm_skeletonisation - iterative skeletonisation using dm (see DM program)
• matthews_coef - Misha Isupov's Jiffy to calculate Matthews coefficient
• ncsmask - averaging mask manipulation program
• parrot - density modification package
• professs - determination of NCS operators from heavy atoms
• solomon - density modification (phase improvement) by solvent flipping

EXPERIMENTAL PHASING

• crank - Automated structure solution for experimental phasing
• rantan - Direct Method module for the determination of heavy atom positions

MAP CALCULATION AND MANIPULATION

• edstats - Calculate electron density statistics
• extends - Extend Fourier maps and compute standard uncertainty of electron density
• fft - fast Fourier transform
• 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
• maptona4 - Convert binary map file to and from na4 ascii format
• omit - program to calculate omit-maps according to Bhat procedure
• overlapmap - calculates the average of two maps
• peakmax - search for peaks in the electron density map
• sigmaa - Improved Fourier coefficients using calculated phases
• xdlmapman - manipulation, analysis and reformatting of electron density maps (X-windows tool)

MAXIMUM LIKELIHOOD PHASING

• phaser-2.5.5 - Molecular Replacement, SAD Phasing, Anisotropy Correction, Cell Content Analysis, Translational NCSand Twin Analysis

MODEL ANALYSIS

• act - analyse coordinates
• areaimol - Analyse solvent accessible areas (supported)
• baverage - averages B over main and side chain atoms
• cavenv - Visualise cavities in macromolecular structures
• contact - computes various types of contacts in protein structures
• distang - Distances and angles calculation
• dyndom - determine dynamic domains when two conformations are available
• ncont - computes various types of contacts in protein structures
• polypose - program for superimposing many multi-domain structures
• procheck - programs to check the Stereochemical Quality of Protein Structures
• rampage - Ramachandran plots
• rotamer - List amino acids whose side chain torsion angles deviate from the Penultimate Rotamer Library
• rotamer table - rotamer tables used in the `rotamer' program
• sc - analyse shape complementarity (supported)
• seqwt - Calculate molecular weight from sequence
• sfcheck - program for assessing the agreement between the atomic model and X-ray data
• surface - surface accessibility program and for preparing input file to program volume
• topp - a topological comparison program
• volume - polyhedral volume around selected atoms

MODEL REFINEMENT

• anisoanl - analyses of anisotropic displacement parameters
• arp_waters - Automated Refinement Procedure for refining protein structures
• dimple - automated difference map calculation
• intro_mon_lib - description of monomer library used in CCP4
• libcheck - monomer library management program
• lib_list - contents of multi-purpose monomer dictionary used by REFMAC
• mon_lib - description of multi-purpose monomer dictionary used by REFMAC
• rdent - Create dictionary entries for Restrain from PDB file
• refmac5 - macromolecular refinement program
• restrain - macromolecular refinement program
• sfall - Structure factor calculation and X-ray refinement using forward and reverse FFT
• sketcher - monomer library sketcher
• tlsanl - analysis of TLS tensors and derived anisotropic U factors
• tlsextract - extract TLS group description from a PDB file
• watncs - Pick waters which follow NCS and sort out to NCS asymmetric unit

MOLECULAR REPLACEMENT

• almn - calculates rotation function overlap values using FFT techniques (alternative to AMORE)
• amore - Jorge Navaza's state-of-the-art molecular replacement package
• beast - Likelihood-based molecular replacement
• bulk - bulk solvent correction for translation search and rigid body refinement steps of AMoRe
• ecalc - calculate normalised structure amplitudes
• fsearch - 6-d molecular replacement (envelope) search
• getax - real space correlation search
• molrep - automated program for molecular replacement
• mrbump - automated search model generation and automated molecular replacement
• polarrfn - fast rotation function that works in polar angles
• rfcorr - Analysis of correlations between cross- and self-Rotation functions
• rotmat - interconverts CCP4/MERLOT/X-PLOR rotation angles
• rsearch - R-factor and correlation coefficient between Fcalc and Fobs
• seqwt - Calculate molecular weight from sequence
• tffc - Translation Function Fourier Coefficients

MTZ MANIPULATIONS / CONVERSIONS

• cad - Collect and sort crystallographic reflection data from several files
• cif2mtz - Convert an mmCIF reflection file to MTZ format
• convert2mtz - CNS to MTZ conversion
• cphasematch - Calculate agreement between phase sets
• ecalc - calculate normalised structure amplitudes
• f2mtz - Convert a formatted reflection file to MTZ format
• freerflag - tags each reflection in an MTZ file with a flag for cross-validation
• freerunique - convert FreeRflags between CCP4 and other formats (see freerflag,uniqueify,mtz2various,f2mtz)
• 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
• mtzdump - dump data from an MTZ reflection data file
• mtzMADmod - Generate F+/F- or F/D from other for anomalous data
• 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
• sftools - reflection data file utility program
• sortmtz - Sort a MTZ reflection data file
• xdldataman - manipulation, analysis and reformatting of reflection files (X-windows tool)

MULTIMER ANALYSIS

• pisa - Protein interfaces, surfaces and assemblies

MULTIPLE ISOMORPHOUS REPLACEMENT

• abs - determine the absolute configuration (hand) of the heavy atom substructure
• afro - multivariate substructure factor amplitude estimation for SAD/MAD and SIRAS
• bp3 - multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
• findncs - detect NCS operations automatically from heavy atom sites
• gcx - support program to generate crank XML and run crank via a script
• mlphare - maximum likelihood heavy atom refinement and phase calculation
• oasis - A program for breaking phase ambiguity in OAS or SIR
• peakmax - search for peaks in the electron density map
• rsps - heavy atom positions from derivative difference Patterson maps
• sapi - heavy atom site location
• vecref - Vector-space refinement of heavy atom sites in isomorphous derivatives
• vecsum - Program to deconvolute a Patterson function and solve the structure (unsupported)
• vectors - generates Patterson vectors from atomic coordinates

MULTIWAVELENGTH ANOMALOUS DISPERSION

• abs - determine the absolute configuration (hand) of the heavy atom substructure
• afro - multivariate substructure factor amplitude estimation for SAD/MAD and SIRAS
• bp3 - multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
• crossec - interpolate X-ray cross sections and compute anomalous scattering factors
• gcx - support program to generate crank XML and run crank via a script
• mlphare - maximum likelihood heavy atom refinement and phase calculation
• oasis - A program for breaking phase ambiguity in OAS or SIR
• revise - estimates optimised value of the normalised anomalous scattering using MAD data
• sapi - heavy atom site location

NATIVE PROTEIN DATA AT ATOMIC RESOLUTION

• acorn - Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure

OTHERS/JIFFIES

• phistats - Analysis of agreement between phase sets, and checking it against weighting factors
• 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
• tracer - Lattice TRAnsformation and CEll Reduction

PLOTTING / GRAPHICS

• openastexviewer - Java program for display molecular structures and electron density maps
• ccp4mapwish - custom wish interpreter required for MapSlicer
• hklplot - plots a precession photo from an HKL data file
• hklview - displays zones of reciprocal space as pseudo-precession images (X-windows program)
• ipdisp - displays images from a variety of (crystallographic) sources (X-Windows tool)
• loggraph - viewer for CCP4 formatted `log' files
• mapslicer - interactive section viewer for CCP4 map files
• npo - Molecule and map plotting
• pltdev - convert Plot84 meta-files to PostScript, Tektronix or HPGL
• topdraw - Sketchpad for protein topology diagrams (supported)
• xloggraph - a viewer of specially formatted `log' files (X-windows tool)
• xplot84driver - a viewer for Plot84 meta files (X-windows tool)

PROTEIN SEQUENCE FILE MANIPULATIONS

• clustalw interface - Graphical Interface to the ClustalW Program
• import/edit protein sequence - Import and edit protein sequences

ROTATION MATRICES

• rotationmatrices - on Eulerian angles, polar angles and direction cosines, and orthogonalisation codes

SCALING DATA

• fhscal - Scaling of isomorphous derivative data using Kraut's method (see also SCALEIT)
• icoefl - vectorially combined scaling of Fobs (Iobs) with partial Fc's
• rstats - scale together two sets of F's
• scalechoose - information about choice of scaling program (see reindex)
• scaleit - derivative to native scaling (see also FHSCAL)

SYMMETRY UTILITIES

• symconv - Fetch and convert symmetry and spacegroup information

VALIDATION AND DEPOSITION

• data harvesting manager - Tool for managing Data Harvesting Files
• pdb_extract - RCSB/PDB Programs for extracting harvest information from program log files
• r500 - Checks PDB files for any problems before submission