CCP4 Program DocumentationCCP4 v5.0.2 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 ccp4 - introduction to the CCP4 Program Suite ccp4i - interface to the CCP4 programs & file display ccp4_installation - Installation of CCP4 suite ccp4_interface_installation - Installation of CCP4 Interface FILE FORMATS intro_mon_lib - description of monomer library used in CCP4 mmcifformat - mmCIF file format as used in CCP4 mtzformat - MTZ file format for CCP4 pdbformat - PDB file format for CCP4 GENERAL alternate_origins - lists of alternate origins for different spacegroups 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 reindexing - information about changing indexing regime scalechoose - information about choice of scaling program symmetry - overview of symmetry information twinning - dealing with data from twinned crystals tutorial - tutorial material for CCP4 suite including Data Processing, MAD phasing, Molecular Replacement and Refinement ccp4 roadmaps - roadmaps through the stages of structure determination using the CCP4 suite pxmaths - Basic Maths for Protein Crystallographers LIBRARY cciflib - Subroutine Library for handling CCIF files ccplib - utility subroutine 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 libhtml - Subroutine Library for inserting html tags into log files lib_list - contents of multi-purpose monomer dictionary used by REFMAC 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 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 c libraries - CCP4 C/C++ Software Library 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 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 arp_waters - Automated Refinement Procedure for refining protein structures astexviewer - Java program for display molecular structures and electron density maps baverage - averages B over main and side chain atoms beast - Likelihood-based molecular replacement bones2pdb - Make a PDB pseudo-coordinate file from a bones file bplot - Plot temperature factor by residue 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 - Calculates cavities in macromolecular structures ccp4mapwish - custom wish interpreter required for MapSlicer 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 coordconv - Interconvert various coordinate formats coord_format - fix PDB format and convert to/from other formats crossec - interpolate X-ray cross sections and compute anomalous scattering factors cross_validate - Validation of harvest files for deposition detwin - detwins merohedrally twinned data data harvesting manager - Tool for managing Data Harvesting Files 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 gensym - generate sites by symmetry geomcalc - molecular geometry calculations getax - real space correlation search import/edit protein sequence - Import and edit protein sequences 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 icoefl - vectorially combined scaling of Fobs (Iobs) with partial Fc's ipdisp - displays images from a variety of (crystallographic) sources 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 6 for processing image plate and CCD data 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 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 pdbcur - various useful manipulations on coordinate files pdb_extract - RCSB/PDB Programs for extracting harvest information from program log files pdbset - various useful manipulations on coordinate files peakmax - search for peaks in the electron density map phistats - Analysis of agreement between phase sets, and checking it against weighting factors pltdev - convert Plot84 meta-files to PostScript, Tektronix or HPGL polarrfn - fast rotation function that works in polar angles polypose - program for superimposing many multi-domain structures procheck - programs to check the Stereochemical Quality of Protein Structures professs - determination of NCS operators from heavy atoms rantan - Direct Method module for the determination of heavy atom positions rasmol - Molecular Visualisation Program rdent - Create dictionary entries for Restrain from PDB file 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 restrain - macromolecular refinement program 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 rsearch - R-factor and correlation coefficient between Fcalc and Fobs 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 scala - scale together multiple observations of reflections scaleit - derivative to native scaling scalepack2mtz - converts merged scalepack output into MTZ format sc - analyse shape complementarity 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 surface - surface accessibility program and for preparing input file to program volume 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 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 xplot84driver - a viewer for Plot84 meta files UNSUPPORTED angles - bond lengths, bond angles and dihedral angles from coordinate files axissearch - Check short reciprocal lattive 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 mapexchange - convert map between binary and formatted mapreplace - Combine parts of 2 maps p842asc - Read and write plot84 and ascii files postref - Post-refinement of reflection data refindex - reindex dataset maximising correlation with reference dataset reforigin - apply best origin shift to PDB atom co-ords according to reference file rotaprep - produces an MTZ file in multirecord form suitable for input to SCALA. vecsum - program to deconvolute a Patterson function and solve the structure zeroed - Set parts of map to zero Penn State Milton S. Hershey Medical Center ©2004 This page was last updated on May 09, 2005 Contact Us