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CCP4 v4.2.2 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 alphabetical order.

COORDINATE FILE MANIPULATIONS

  • bones2pdb - Make a PDB pseudo-coordinate file from a bones file
  • coordconv - Interconvert various coordinate formats
  • gensym - generate sites by symmetry
  • geomcalc - molecular geometry calculations
  • import/edit protein sequence - Import and edit protein sequences
  • 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
  • pdbset - various useful manipulations on coordinate files
  • rwcontents - Count atoms by type
  • sortwater - sort waters by the protein chain to which they "belong"
  • 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

  • harvesting - harvesting data automatically and using datasets

DATA PROCESSING AND REDUCTION

  • absurd - initial processing of intensity files from MADNES
  • combat - produces an MTZ file in multirecord form suitable for input to SCALA.
  • crossec - interpolate X-ray cross sections and compute anomalous scattering factors
  • detwin - detwins merohedrally twinned data
  • dtrek2mtz - converts d*trek scalemerge output into MTZ format
  • 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
  • undupl - remove duplicates from Madnes data, after Absurd
  • unique - Generate a unique list of reflections (including uniqueify)
  • wilson - Wilson plot, absolute scale and temperature factor

DENSITY FITTING AND MODEL BUILDING

DENSITY MODIFICATION - MOLECULAR AVERAGING

  • dm - density modification package
  • dm_ncs_averaging - dm for ncs averaging (see DM program)
  • dm_skeletonisation - iterative skeletonisation using dm (see DM program)
  • dmmulti - multi-xtal density modification package
  • matthews_coef - Misha Isupov's Jiffy to calculate Matthews coefficient
  • ncsmask - averaging mask manipulation program
  • professs - determination of NCS operators from heavy atoms
  • solomon - density modification (phase improvement) by solvent flipping

MAP CALCULATION AND MANIPULATION

  • 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)

MODEL ANALYSIS

  • act - analyse coordinates
  • areaimol - Analyse solvent accessible areas (supported)
  • baverage - averages B over main and side chain atoms
  • cavenv - Calculates 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
  • polypose - program for superimposing many multi-domain structures
  • procheck - programs to check the Stereochemical Quality of Protein Structures
  • 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)
  • 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
  • intro_mon_lib - description of monomer library used in CCP4
  • lib_list - contents of multi-purpose monomer dictionary used by REFMAC
  • libcheck - monomer library management program
  • mon_lib - description of multi-purpose monomer dictionary used by REFMAC
  • protin - (not required, use new refmac)
  • rdent - Create dictionary entries for Restrain from PDB file
  • refmac - (old version, use refmac5)
  • refmac5 - macromolecular refinement program
  • restrain - macromolecular refinement program
  • sfall - Structure factor calculation and X-ray refinement using forward and reverse FFT
  • tlsanl - analysis of TLS tensors and derived anisotropic U factors
  • 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
  • ecalc - calculate normalised structure amplitudes
  • fsearch - 6-d molecular replacement (envelope) search
  • getax - real space correlation search
  • molrep - automated program for molecular replacement
  • polarrfn - fast rotation function which 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
  • 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
  • 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)
  • mtz2various - produces reflexion file for MULTAN, SHELX, TNT, X-PLOR/CNS, CIF 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
  • 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)

MULTIPLE ISOMORPHOUS REPLACEMENT

  • abs - determine the absolute configuration (hand) of the heavy atom substructure
  • findncs - detect NCS operations automatically from heavy atom sites
  • 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
  • crossec - interpolate X-ray cross sections and compute anomalous scattering factors
  • mlphare - maximum likelihood heavy atom refinement and phase calculation
  • oasis - A program for breaking phase ambiguity in OAS or SIR
  • rantan - Direct Method module for the determination of heavy atom positions
  • 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

  • astexviewer - 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
  • rasmol - Molecular Visualisation Program (X-windows tool)
  • xloggraph - a viewer of specially formatted `log' files (X-windows tool)
  • xplot84driver - a viewer for Plot84 meta files (X-windows tool)

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)