CCP4 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 alphabetical order.
COORDINATE FILE MANIPULATIONS
- bones2pdb - Make a PDB pseudo-coordinate file from a bones file
- clustalw interface - Graphical Interface to the ClustalW Program
- coordconv - Interconvert various coordinate formats
- coord_format - fix PDB format and convert to/from other formats
- gensym - generate sites by symmetry
- geomcalc - molecular geometry calculations
- 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
- pdbcur - various useful manipulations on coordinate files
- 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
- cif2xml - Conversion of mmCIF files to XML
- cross_validate - Validation of harvest files for deposition
- data harvesting manager - Tool for managing Data Harvesting Files
- harvesting - harvesting data automatically and using datasets
- harvlib - Subroutine library for writing CIF harvest files
- pdb_extract - RCSB/PDB Programs for extracting harvest information from program log files
DATA PROCESSING AND REDUCTION
- 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
- dtrek2scala - initial processing of intensity files from D*TREK
- 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
- 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
- dmmulti - multi-xtal density modification package
- dm_ncs_averaging - dm for ncs averaging (see DM program)
- dm_skeletonisation - iterative skeletonisation using dm (see DM program)
- 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
- extends - Extend Fourier maps and compute standard uncertainty of electron density
- 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
- ncont - computes various types of contacts in protein structures
- 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
- libcheck - monomer library management program
- lib_list - contents of multi-purpose monomer dictionary used by REFMAC
- mon_lib - description of multi-purpose monomer dictionary used by REFMAC
- rdent - Create dictionary entries for Restrain from PDB file
- refmac5 - macromolecular refinement program
- restrain - macromolecular refinement program
- sfall - Structure factor calculation and X-ray refinement using forward and reverse FFT
- sketcher - monomer library sketcher
- tlsanl - analysis of TLS tensors and derived anisotropic U factors
- tlsextract - extract TLS group description from a PDB file
- 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
- bulk - bulk solvent correction for translation search and rigid body refinement steps of AMoRe
- 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 that 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, 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
- 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)
- topdraw - Sketchpad for protein topology diagrams (supported)
- xloggraph - a viewer of specially formatted `log' files (X-windows tool)
- xplot84driver - a viewer for Plot84 meta files (X-windows tool)
PROTEIN SEQUENCE FILE MANIPULATIONS
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)
VALIDATION AND DEPOSITION