abs (CCP4) - determine the absolute configuration (hand) of the heavy atom substructure acorn (CCP4) - Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure act (CCP4) - analyse coordinates afro (CCP4) - multivariate substructure factor amplitude estimation for SAD/MAD and SIRAS aimless (CCP4) - scale together multiple observations of reflections almn (CCP4) - calculates rotation function overlap values using FFT techniques alternate_origins (CCP4)- list of alternate origins for enantiomorphic spacegroups alternate_origins_allgroups (CCP4)- list of alternate origins for different spacegroups amore (CCP4) - Jorge Navaza's state-of-the-art molecular replacement package angles (CCP4) - Bond lengths, bond angles and dihedral angles from coordinate files anisoanl (CCP4) - analyses of anisotropic displacement parameters areaimol (CCP4) - Analyse solvent accessible areas arp_waters (CCP4) - Automated Refinement Procedure for refining protein structures axissearch (CCP4) - Check short reciprocal lattice vectors- there may be an alternative definition of unit cell baverage (CCP4) - averages B over main and side chain atoms beast (CCP4) - Likelihood-based molecular replacement blend (CCP4) - multi-dataset combination and cluster analysis bones2pdb (CCP4) - Make a PDB pseudo-coordinate file from a bones file bp3 (CCP4) - multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD bplot (CCP4) - Plot temperature factor by residue buccaneer (CCP4) - Statistical Model Building bulk (CCP4) - bulk solvent correction for translation search and rigid body refinement steps of AMoRe c libraries (CCP4) - CCP4 C/C++ Software Library cad (CCP4) - Collect and sort crystallographic reflection data from several files cavenv (CCP4) - Visualise cavities in macromolecular structures cciflib (CCP4) - Subroutine Library for handling CCIF files ccp4 (CCP4) - introduction to the CCP4 Program Suite ccp4 roadmaps (CCP4) - roadmaps through the stages of structure determination using the CCP4 suite ccp4_interface_installation (CCP4)- Installation of CCP4 Interface ccp4i (CCP4) - interface to the CCP4 programs & file display ccp4mapwish (CCP4) - custom wish interpreter required for MapSlicer ccplib (CCP4) - utility subroutine library chainsaw (CCP4) - Mutate a pdb file according to an input sequence alignment cheshire cells (CCP4) - background information on Cheshire Cells and their uses cif2mtz (CCP4) - Convert an mmCIF reflection file to MTZ format cif2xml (CCP4) - Conversion of mmCIF files to XML clustalw interface (CCP4)- Graphical Interface to the ClustalW Program cmakereference (CCP4) - Generate reference structure for pirate/buccaneer cmap library (CCP4) - C/C++ Software Library for CCP4 map files cmapcut (CCP4) - Prepare MR density search cmtz library (CCP4) - C/C++ Software Library for MTZ files combat (CCP4) - produces an MTZ file in multirecord form suitable for input to SCALA. comit (CCP4) - Composite omit maps compar (CCP4) - Comparison of coordinates contact (CCP4) - computes various types of contacts in protein structures convert2mtz (CCP4) - CNS to MTZ conversion coord_format (CCP4) - fix PDB format and convert to/from other formats coordconv (CCP4) - Interconvert various coordinate formats cparser library (CCP4) - C Software Library for CCP4-style parsing cphasematch (CCP4) - Calculate agreement between phase sets crank (CCP4) - Automated structure solution for experimental phasing cross_validate (CCP4) - Validation of harvest files for deposition crossec (CCP4) - interpolate X-ray cross sections and compute anomalous scattering factors csym library (CCP4) - C/C++ Software Library for symmetry information csymmatch (CCP4) - Use symmetry to match chains ctruncate (CCP4) - Intensity to amplitude conversion data harvesting manager (CCP4)- Tool for managing Data Harvesting Files detwin (CCP4) - detwins merohedrally twinned data diffraction image (CCP4)- CCP4 Diffraction Image Handling Library dimple (CCP4) - automated difference map calculation diskio (CCP4) - low-level input/output subroutine library distang (CCP4) - Distances and angles calculation dm (CCP4) - density modification package dm_ncs_averaging (CCP4) - dm for ncs averaging dm_skeletonisation (CCP4)- iterative skeletonisation using dm dmmulti (CCP4) - multi-xtal density modification package dna_output (CCP4) - DNA library for XML output from programs dtrek2mtz (CCP4) - converts d*trek scalemerge output into MTZ format dtrek2scala (CCP4) - initial processing of intensity files from D*TREK dyndom (CCP4) - determine dynamic domains when two conformations are available ecalc (CCP4) - calculate normalised structure amplitudes edstats (CCP4) - Calculate electron density statistics extends (CCP4) - Extend Fourier maps and compute standard uncertainty of electron density f2mtz (CCP4) - Convert a formatted reflection file to MTZ format fffear (CCP4) - map interpretation package fffear fragment library (CCP4)- map interpretation package ffjoin (CCP4) - joining model fragments from FFFEAR fft (CCP4) - fast Fourier transform fhscal (CCP4) - Scaling of isomorphous derivative data using Kraut's method findncs (CCP4) - detect NCS operations automatically from heavy atom sites freerflag (CCP4) - tags each reflection in an MTZ file with a flag for cross-validation freerunique (CCP4) - convert FreeRflags between CCP4 and other formats fsearch (CCP4) - 6-d molecular replacement (envelope) search gcx (CCP4) - support program to generate crank XML and run crank via a script gensym (CCP4) - generate sites by symmetry geomcalc (CCP4) - molecular geometry calculations gesamt (CCP4) - structural alignment getax (CCP4) - real space correlation search harvesting (CCP4) - harvesting data automatically and using datasets harvlib (CCP4) - Subroutine library for writing CIF harvest files havecs (CCP4) - Generate heavy atom vectors helixang (CCP4) - Program to calculate contacts, angles and separations between helices. hgen (CCP4) - generate hydrogen atom positions for proteins hklplot (CCP4) - plots a precession photo from an HKL data file hklview (CCP4) - displays zones of reciprocal space as pseudo-precession images hltofom (CCP4) - Convert to/from Hendrickson-Lattman coefficients icoefl (CCP4) - vectorially combined scaling of Fobs (Iobs) with partial Fc's import/edit protein sequence (CCP4)- Import and edit protein sequences intro_mon_lib (CCP4) - description of monomer library used in CCP4 ipdisp (CCP4) - displays images from a variety of (crystallographic) sources keyparse (CCP4) - high-level keyword parsing subroutines lib_list (CCP4) - contents of multi-purpose monomer dictionary used by REFMAC libcheck (CCP4) - monomer library management program libhtml (CCP4) - Subroutine Library for inserting html tags into log files library (CCP4) - low-level C subroutine library loggraph (CCP4) - viewer for CCP4 formatted `log' files loggraphformat (CCP4) - Loggraph file format for CCP4 lsqkab (CCP4) - apply various transformations to coordinate files makedict (CCP4) - converts PDB file to TNT or PROTIN dictionaries and PROTIN to PDB mama2ccp4 (CCP4) - Convert between `mama' and Cambridge/CCP4 map formats map2fs (CCP4) - convert CCP4 map to XtalView fsfour format mapdump (CCP4) - print a dump of sections of a map file mapexchange (CCP4) - Convert map between binary and formatted maplib (CCP4) - Subroutine Library for CCP4 map file handling mapmask (CCP4) - map/mask extend program mapreplace (CCP4) - Combine parts of 2 maps maprot (CCP4) - map skewing, interpolating, rotating, averaging and correlation masking program mapsig (CCP4) - print statistics on signal/noise for translation function map mapslicer (CCP4) - interactive section viewer for CCP4 map files maptona4 (CCP4) - Convert binary map file to and from na4 ascii format matthews_coef (CCP4) - Misha Isupov's Jiffy to calculate Matthews coefficient mlphare (CCP4) - maximum likelihood heavy atom refinement and phase calculation mmcifformat (CCP4) - mmCIF file format as used in CCP4 modlib (CCP4) - Subroutine Library for mathematical operations molrep (CCP4) - automated program for molecular replacement mon_lib (CCP4) - description of multi-purpose monomer dictionary used by REFMAC mosflm (CCP4) - MOSFLM version 7 for processing image plate and CCD data mrbump (CCP4) - automated search model generation and automated molecular replacement mtz2cif (CCP4) - produce mmCIF structure factor file suitable for deposition mtz2sca (CCP4) - Convert CCP4 mtz-files containing anomalous data to Scalepack format mtz2various (CCP4) - produces reflexion file for MULTAN, SHELX, TNT, X-PLOR/CNS, pseudo-SCALEPACK, XtalView, mmCIF or other ascii format mtzMADmod (CCP4) - Generate F+/F- or F/D from other for anomalous data mtzdump (CCP4) - dump data from an MTZ reflection data file mtzformat (CCP4) - MTZ file format for CCP4 mtzlib (CCP4) - Fortran Software Library for Reflection data file handling mtzmnf (CCP4) - Identify missing data entries in an MTZ file and replace with a Missing Number Flag (MNF) mtztona4 (CCP4) - interconvert MTZ reflection file and ASCII format mtzutils (CCP4) - Reflection data files utility program nautilus (CCP4) - Statistical Model Building ncont (CCP4) - computes various types of contacts in protein structures ncsmask (CCP4) - averaging mask manipulation program non-centro_origins (CCP4)- lists of alternate origins for non-centrosymetric spacegroups npo (CCP4) - Molecule and map plotting oasis (CCP4) - A program for breaking phase ambiguity in OAS or SIR omit (CCP4) - program to calculate omit-maps according to Bhat procedure openastexviewer (CCP4) - Java program for display molecular structures and electron density maps othercell (CCP4) - explore equivalent alternative unit cells overlapmap (CCP4) - calculates the average of two maps p842asc (CCP4) - Read and write plot84 and ascii files parrot (CCP4) - density modification package parser (CCP4) - parser subroutine library pdb_extract (CCP4) - RCSB/PDB Programs for extracting harvest information from program log files pdb_merge (CCP4) - merge two coordinate files into one pdbcur (CCP4) - various useful manipulations on coordinate files pdbformat (CCP4) - PDB file format for CCP4 pdbset (CCP4) - various useful manipulations on coordinate files peakmax (CCP4) - search for peaks in the electron density map phaser-2.5.5 (CCP4) - Molecular Replacement, SAD Phasing, Anisotropy Correction, Cell Content Analysis, Translational NCSand Twin Analysis phistats (CCP4) - Analysis of agreement between phase sets, and checking it against weighting factors pirate (CCP4) - Statistical Phase Improvement pisa (CCP4) - Protein interfaces, surfaces and assemblies pltdev (CCP4) - convert Plot84 meta-files to PostScript, Tektronix or HPGL pointless (CCP4) - determine Laue group polarrfn (CCP4) - fast rotation function that works in polar angles polypose (CCP4) - program for superimposing many multi-domain structures postref (CCP4) - Post-refinement of reflection data prelyscar (CCP4) - Predictor of Lysine Carboxylation privateer (CCP4) - Validation of carbohydrate structures procheck (CCP4) - programs to check the Stereochemical Quality of Protein Structures prodrg (CCP4) - generation of small molecule coordinates professs (CCP4) - determination of NCS operators from heavy atoms prosmart (CCP4) - Comparison of chains, and restraints generation pxmaths (CCP4) - Basic Maths for Protein Crystallographers pxxml (CCP4) - Subroutine Library for writing XML r500 (CCP4) - Checks PDB files for any problems before submission rampage (CCP4) - Ramachandran plots rantan (CCP4) - Direct Method module for the determination of heavy atom positions rapper (CCP4) - conformer modelling and building rdent (CCP4) - Create dictionary entries for Restrain from PDB file rebatch (CCP4) - alter batch numbers in an unmerged MTZ file refindex (CCP4) - Reindex dataset maximising correlation with reference dataset refmac5 (CCP4) - macromolecular refinement program reforigin (CCP4) - Apply best origin shift to PDB atom co-ords according to reference file reindex (CCP4) - produces an MTZ file with h k l reindexed and/or the symmetry changed reindexing (CCP4) - information about changing indexing regime restrain (CCP4) - macromolecular refinement program revise (CCP4) - estimates optimised value of the normalised anomalous scattering using MAD data rfcorr (CCP4) - Analysis of correlations between cross- and self-Rotation functions rotamer (CCP4) - List amino acids whose side chain torsion angles deviate from the Penultimate Rotamer Library rotamer table (CCP4) - rotamer tables used in the `rotamer' program rotaprep (CCP4) - produces an MTZ file in multirecord form suitable for input to SCALA. rotationmatrices (CCP4) - on Eulerian angles, polar angles and direction cosines, and orthogonalisation codes rotgen (CCP4) - Program to simulate X-ray diffraction rotation images rotmat (CCP4) - interconverts CCP4/MERLOT/X-PLOR rotation angles rsearch (CCP4) - R-factor and correlation coefficient between Fcalc and Fobs rsps (CCP4) - heavy atom positions from derivative difference Patterson maps rstats (CCP4) - scale together two sets of F's rwbrook (CCP4) - Library Subroutines for handling the co-ordinate working format rwcontents (CCP4) - Count atoms by type sapi (CCP4) - heavy atom site location sc (CCP4) - analyse shape complementarity scala (CCP4) - scale together multiple observations of reflections scalechoose (CCP4) - information about choice of scaling program scaleit (CCP4) - derivative to native scaling scalepack2mtz (CCP4) - converts merged scalepack output into MTZ format sequins (CCP4) - Statistical Model Building seqwt (CCP4) - Calculate molecular weight from sequence sfall (CCP4) - Structure factor calculation and X-ray refinement using forward and reverse FFT sfcheck (CCP4) - program for assessing the agreement between the atomic model and X-ray data sftools (CCP4) - reflection data file utility program sigmaa (CCP4) - Improved Fourier coefficients using calculated phases sketcher (CCP4) - monomer library sketcher solomon (CCP4) - density modification (phase improvement) by solvent flipping sortmtz (CCP4) - Sort a MTZ reflection data file sortwater (CCP4) - sort waters by the protein chain to which they "belong" stereo (CCP4) - Extract coordinates from stereo diagrams stgrid (CCP4) - Generate plot to measure angular coordinates on a stereographic projection from polarrfn stnet (CCP4) - Generate plot to measure angles between points on a stereographic projection from polarrfn superpose (CCP4) - structural alignment based on secondary structure matching surface (CCP4) - surface accessibility program and for preparing input file to program volume symconv (CCP4) - Fetch and convert symmetry and spacegroup information symlib (CCP4) - Fortran Software Library for handling symmetry operations symmetry (CCP4) - overview of symmetry information tffc (CCP4) - Translation Function Fourier Coefficients tlsanl (CCP4) - analysis of TLS tensors and derived anisotropic U factors tlsextract (CCP4) - extract TLS group description from a PDB file topdraw (CCP4) - Sketchpad for protein topology diagrams topp (CCP4) - a topological comparison program tracer (CCP4) - Lattice TRAnsformation and CEll Reduction truncate (CCP4) - obtain structure factor amplitudes using Truncate procedure tutorial (CCP4) - tutorial material for CCP4 suite including Data Processing, MAD phasing, Molecular Replacement and Refinement twinning (CCP4) - dealing with data from twinned crystals unique (CCP4) - Generate a unique list of reflections unix.m4 (CCP4) - library routines for system interactions vecref (CCP4) - Vector-space refinement of heavy atom sites in isomorphous derivatives vecsum (CCP4) - Program to deconvolute a Patterson function and solve the structure vectors (CCP4) - generates Patterson vectors from atomic coordinates volume (CCP4) - polyhedral volume around selected atoms watertidy (CCP4) - rationalise waters at the end of refinement watncs (CCP4) - Pick waters which follow NCS and sort out to NCS asymmetric unit watpeak (CCP4) - selects peaks from peakmax and puts them close to the respective protein atoms wilson (CCP4) - Wilson plot, absolute scale and temperature factor xdl_view (CCP4) - X-windows based toolkit xdldataman (CCP4) - manipulation, analysis and reformatting of reflection files xdlmapman (CCP4) - manipulation, analysis and reformatting of electron density maps xia2 (CCP4) - Automated data reduction xloggraph (CCP4) - a viewer of specially formatted `log' files xplot84driver (CCP4) - a viewer for Plot84 meta files zeroed (CCP4) - Set parts of map to zero