•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