ccp4 functions

•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
•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
•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
•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
•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
•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