View source for List of ccp4 programs

 see: [http://www.ccp4.ac.uk/dist/html/ CCP4 v6.0.2 Program Documentation]

==Coordinate file manipulations==

;[http://www.ccp4.ac.uk/dist/html/bones2pdb.html bones2pdb] : Make a PDB pseudo-coordinate file from a bones file
;[http://www.ccp4.ac.uk/dist/html/chainsaw.html chainsaw] : Mutate a pdb file according to an input sequence alignment
;[http://www.ccp4.ac.uk/dist/html/clustalw.html clustalw interface] : Graphical Interface to the ClustalW Program
;[http://www.ccp4.ac.uk/dist/html/coordconv.html coordconv] : Interconvert various coordinate formats
;[http://www.ccp4.ac.uk/dist/html/coord_format.html coord_format] : fix PDB format and convert to/from other formats
;[http://www.ccp4.ac.uk/dist/html/gensym.html gensym] : generate sites by symmetry
;[http://www.ccp4.ac.uk/dist/html/geomcalc.html geomcalc] : molecular geometry calculations
;[http://www.ccp4.ac.uk/dist/html/hgen.html hgen] : generate hydrogen atom positions for proteins
;[http://www.ccp4.ac.uk/dist/html/lsqkab.html lsqkab] : apply various transformations to coordinate files
;[http://www.ccp4.ac.uk/dist/html/makedict.html makedict] : converts PDB file to TNT or PROTIN dictionaries and PROTIN to PDB
;[http://www.ccp4.ac.uk/dist/html/pdbcur.html pdbcur] : various useful manipulations on coordinate files
;[http://www.ccp4.ac.uk/dist/html/pdb_merge.html pdb_merge] : merge two coordinate files into one
;[http://www.ccp4.ac.uk/dist/html/pdbset.html pdbset] : various useful manipulations on coordinate files
;[http://www.ccp4.ac.uk/dist/html/reforigin.html reforigin] : apply best origin shift to PDB atom co-ords according to reference file (unsupported)
;[http://www.ccp4.ac.uk/dist/html/rwcontents.html rwcontents] : Count atoms by type
;[http://www.ccp4.ac.uk/dist/html/sortwater.html sortwater] : sort waters by the protein chain to which they "belong"
;[http://www.ccp4.ac.uk/dist/html/superpose.html superpose] : structural alignment based on secondary structure matching
;[http://www.ccp4.ac.uk/dist/html/watertidy.html watertidy] : rationalise waters at the end of refinement
;[http://www.ccp4.ac.uk/dist/html/watpeak.html watpeak] : selects peaks from peakmax and puts them close to the respective protein atoms

==Data harvesting and datasets==

;[http://www.ccp4.ac.uk/dist/html/cif2xml.html cif2xml] : Conversion of mmCIF files to XML
;[http://www.ccp4.ac.uk/dist/html/cross_validate.html cross_validate] : Validation of harvest files for deposition
;[http://www.ccp4.ac.uk/dist/html/dhm_tool.html data harvesting manager] : Tool for managing Data Harvesting Files
;[http://www.ccp4.ac.uk/dist/html/harvesting.html harvesting] : harvesting data automatically and using datasets
;[http://www.ccp4.ac.uk/dist/html/harvlib.html harvlib] : Subroutine library for writing CIF harvest files
;[http://www.ccp4.ac.uk/dist/html/pdb_extract.html pdb_extract] : RCSB/PDB Programs for extracting harvest information from program log files

==Data processing and reduction==

;[http://www.ccp4.ac.uk/dist/html/combat.html combat] : produces an MTZ file in multirecord form suitable for input to SCALA.
;[http://www.ccp4.ac.uk/dist/html/crossec.html crossec] : interpolate X-ray cross sections and compute anomalous scattering factors
;[http://www.ccp4.ac.uk/dist/html/detwin.html detwin] : detwins merohedrally twinned data
;[http://www.ccp4.ac.uk/dist/html/dtrek2mtz.html dtrek2mtz] : converts d*trek scalemerge output into MTZ format
;[http://www.ccp4.ac.uk/dist/html/dtrek2scala.html dtrek2scala] : initial processing of intensity files from D*TREK
;[http://www.ccp4.ac.uk/dist/html/rebatch.html rebatch] : alter batch numbers in an unmerged MTZ file
;[http://www.ccp4.ac.uk/dist/html/reindex.html reindex] : produces an MTZ file with h k l reindexed and/or the symmetry changed
;[http://www.ccp4.ac.uk/dist/html/reindexing.html reindexing] : information about changing indexing regime (see reindex)
;[http://www.ccp4.ac.uk/dist/html/rotaprep.html rotaprep] : produces an MTZ file in multirecord form suitable for input to SCALA.
;[http://www.ccp4.ac.uk/dist/html/scala.html scala] : scale together multiple observations of reflections
;[http://www.ccp4.ac.uk/dist/html/scalepack2mtz.html scalepack2mtz] : converts merged scalepack output into MTZ format
;[http://www.ccp4.ac.uk/dist/html/truncate.html truncate] : obtain structure factor amplitudes using Truncate procedure
;[http://www.ccp4.ac.uk/dist/html/twinning.html twinning] : dealing with data from twinned crystals
;[http://www.ccp4.ac.uk/dist/html/unique.html unique] : Generate a unique list of reflections (including uniqueify)
;[http://www.ccp4.ac.uk/dist/html/wilson.html wilson] : Wilson plot, absolute scale and temperature factor

==Density fitting and model building==

;[http://www.ccp4.ac.uk/dist/html/arp_waters.html arp_waters] : Automated Refinement Procedure for refining protein structures
;[http://www.ccp4.ac.uk/dist/html/fffear fragment library.html fffear fragment library] : map interpretation package
;[http://www.ccp4.ac.uk/dist/html/fffear.html fffear] : map interpretation package
;[http://www.ccp4.ac.uk/dist/html/ffjoin.html ffjoin] : joining model fragments from FFFEAR

==Density modification : molecular averaging==

;[http://www.ccp4.ac.uk/dist/html/hltofom.html hltofom] : Convert to/from Hendrickson-Lattman coefficients
;[http://www.ccp4.ac.uk/dist/html/pirate.html pirate] : Statistical Phase Improvement
;[http://www.ccp4.ac.uk/dist/html/dm.html dm] : density modification package
;[http://www.ccp4.ac.uk/dist/html/dmmulti.html dmmulti] : multi-xtal density modification package
;[http://www.ccp4.ac.uk/dist/html/dm_ncs_averaging.html dm_ncs_averaging] : dm for ncs averaging (see DM program)
;[http://www.ccp4.ac.uk/dist/html/dm_skeletonisation.html dm_skeletonisation] : iterative skeletonisation using dm (see DM program)
;[http://www.ccp4.ac.uk/dist/html/matthews_coef.html matthews_coef] : Misha Isupov's Jiffy to calculate Matthews coefficient
;[http://www.ccp4.ac.uk/dist/html/ncsmask.html ncsmask] : averaging mask manipulation program
;[http://www.ccp4.ac.uk/dist/html/professs.html professs] : determination of NCS operators from heavy atoms
;[http://www.ccp4.ac.uk/dist/html/solomon.html solomon] : density modification (phase improvement) by solvent flipping

==Experimental phasing==

;[http://www.ccp4.ac.uk/dist/html/acorn.html acorn] : Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure
;[http://www.ccp4.ac.uk/dist/html/crank.html crank] : Automated structure solution for experimental phasing
;[http://www.ccp4.ac.uk/dist/html/rantan.html rantan] : Direct Method module for the determination of heavy atom positions

==Map calculation and manipulation==

;[http://www.ccp4.ac.uk/dist/html/extends.html extends] : Extend Fourier maps and compute standard uncertainty of electron density
;[http://www.ccp4.ac.uk/dist/html/fft.html fft] : fast Fourier transform
;[http://www.ccp4.ac.uk/dist/html/mama2ccp4.html mama2ccp4] : Convert between `mama' and Cambridge/CCP4 map formats
;[http://www.ccp4.ac.uk/dist/html/map2fs.html map2fs] : convert CCP4 map to XtalView fsfour format
;[http://www.ccp4.ac.uk/dist/html/mapdump.html mapdump] : print a dump of sections of a map file
;[http://www.ccp4.ac.uk/dist/html/mapmask.html mapmask] : map/mask extend program
;[http://www.ccp4.ac.uk/dist/html/maprot.html maprot] : map skewing, interpolating, rotating, averaging and correlation masking program
;[http://www.ccp4.ac.uk/dist/html/mapsig.html mapsig] : print statistics on signal/noise for translation function map
;[http://www.ccp4.ac.uk/dist/html/maptona4.html maptona4] : Convert binary map file to and from na4 ascii format
;[http://www.ccp4.ac.uk/dist/html/omit.html omit] : program to calculate omit-maps according to Bhat procedure
;[http://www.ccp4.ac.uk/dist/html/overlapmap.html overlapmap] : calculates the average of two maps
;[http://www.ccp4.ac.uk/dist/html/peakmax.html peakmax] : search for peaks in the electron density map
;[http://www.ccp4.ac.uk/dist/html/sigmaa.html sigmaa] : Improved Fourier coefficients using calculated phases
;[http://www.ccp4.ac.uk/dist/html/xdlmapman.html xdlmapman] : manipulation, analysis and reformatting of electron density maps (X-windows tool)

==Model analysis==

;[http://www.ccp4.ac.uk/dist/html/act.html act] : analyse coordinates
;[[areaimol]] : Analyse solvent accessible areas (supported)
;[http://www.ccp4.ac.uk/dist/html/baverage.html baverage] : averages B over main and side chain atoms
;[http://www.ccp4.ac.uk/dist/html/cavenv.html cavenv] : Calculates cavities in macromolecular structures
;[http://www.ccp4.ac.uk/dist/html/contact.html contact] : computes various types of contacts in protein structures
;[http://www.ccp4.ac.uk/dist/html/distang.html distang] : Distances and angles calculation
;[http://www.ccp4.ac.uk/dist/html/dyndom.html dyndom] : determine dynamic domains when two conformations are available
;[http://www.ccp4.ac.uk/dist/html/ncont.html ncont] : computes various types of contacts in protein structures
;[http://www.ccp4.ac.uk/dist/html/polypose.html polypose] : program for superimposing many multi-domain structures
;[http://www.ccp4.ac.uk/dist/html/procheck.html procheck] : programs to check the Stereochemical Quality of Protein Structures
;[http://www.ccp4.ac.uk/dist/html/rotamer.html rotamer] : List amino acids whose side chain torsion angles deviate from the Penultimate Rotamer Library
;[http://www.ccp4.ac.uk/dist/html/rotamer_table.html rotamer table] : rotamer tables used in the `rotamer' program
;[http://www.ccp4.ac.uk/dist/html/sc.html sc] : analyse shape complementarity (supported)
;[http://www.ccp4.ac.uk/dist/html/sfcheck.html sfcheck] : program for assessing the agreement between the atomic model and X-ray data
;[http://www.ccp4.ac.uk/dist/html/surface.html surface] : surface accessibility program and for preparing input file to program volume
;[http://www.ccp4.ac.uk/dist/html/topp.html topp] : a topological comparison program
;[http://www.ccp4.ac.uk/dist/html/volume.html volume] : polyhedral volume around selected atoms

==Model refinement==

;[http://www.ccp4.ac.uk/dist/html/anisoanl.html anisoanl] : analyses of anisotropic displacement parameters
;[http://www.ccp4.ac.uk/dist/html/arp_waters.html arp_waters] : Automated Refinement Procedure for refining protein structures
;[http://www.ccp4.ac.uk/dist/html/intro_mon_lib.html intro_mon_lib] : description of monomer library used in CCP4
;[http://www.ccp4.ac.uk/dist/html/libcheck.html libcheck] : monomer library management program
;[http://www.ccp4.ac.uk/dist/html/lib_list.html lib_list] : contents of multi-purpose monomer dictionary used by REFMAC
;[http://www.ccp4.ac.uk/dist/html/mon_lib.html mon_lib] : description of multi-purpose monomer dictionary used by REFMAC
;[http://www.ccp4.ac.uk/dist/html/rdent.html rdent] : Create dictionary entries for Restrain from PDB file
;[http://www.ccp4.ac.uk/dist/html/refmac5.html refmac5] : macromolecular refinement program
;[http://www.ccp4.ac.uk/dist/html/restrain.html restrain] : macromolecular refinement program
;[http://www.ccp4.ac.uk/dist/html/sfall.html sfall] : Structure factor calculation and X-ray refinement using forward and reverse FFT
;[http://www.ccp4.ac.uk/dist/html/sketcher.html sketcher] : monomer library sketcher
;[http://www.ccp4.ac.uk/dist/html/tlsanl.html tlsanl] : analysis of TLS tensors and derived anisotropic U factors
;[http://www.ccp4.ac.uk/dist/html/tlsextract.html tlsextract] : extract TLS group description from a PDB file
;[http://www.ccp4.ac.uk/dist/html/watncs.html watncs] : Pick waters which follow NCS and sort out to NCS asymmetric unit

==Molecular replacement==

;[http://www.ccp4.ac.uk/dist/html/almn.html almn] : calculates rotation function overlap values using FFT techniques (alternative to AMORE)
;[http://www.ccp4.ac.uk/dist/html/amore.html amore] : Jorge Navaza's state-of-the-art molecular replacement package
;[http://www.ccp4.ac.uk/dist/html/beast.html beast] : Likelihood-based molecular replacement
;[http://www.ccp4.ac.uk/dist/html/bulk.html bulk] : bulk solvent correction for translation search and rigid body refinement steps of AMoRe
;[http://www.ccp4.ac.uk/dist/html/ecalc.html ecalc] : calculate normalised structure amplitudes
;[http://www.ccp4.ac.uk/dist/html/fsearch.html fsearch] : 6-d molecular replacement (envelope) search
;[http://www.ccp4.ac.uk/dist/html/getax.html getax] : real space correlation search
;[http://www.ccp4.ac.uk/dist/html/molrep.html molrep] : automated program for molecular replacement
;[http://www.ccp4.ac.uk/dist/html/phaser.html phaser] : Maximum Likelihood Phasing
;[http://www.ccp4.ac.uk/dist/html/polarrfn.html polarrfn] : fast rotation function that works in polar angles
;[http://www.ccp4.ac.uk/dist/html/rfcorr.html rfcorr] : Analysis of correlations between cross- and self-Rotation functions
;[http://www.ccp4.ac.uk/dist/html/rotmat.html rotmat] : interconverts CCP4/MERLOT/X-PLOR rotation angles
;[http://www.ccp4.ac.uk/dist/html/rsearch.html rsearch] : R-factor and correlation coefficient between Fcalc and Fobs
;[http://www.ccp4.ac.uk/dist/html/tffc.html tffc] : Translation Function Fourier Coefficients

==MTZ manipulations / conversions==

;[http://www.ccp4.ac.uk/dist/html/cad.html cad] : Collect and sort crystallographic reflection data from several files
;[http://www.ccp4.ac.uk/dist/html/cif2mtz.html cif2mtz] : Convert an mmCIF reflection file to MTZ format
;[http://www.ccp4.ac.uk/dist/html/ecalc.html ecalc] : calculate normalised structure amplitudes
;[http://www.ccp4.ac.uk/dist/html/f2mtz.html f2mtz] : Convert a formatted reflection file to MTZ format
;[http://www.ccp4.ac.uk/dist/html/freerflag.html freerflag] : tags each reflection in an MTZ file with a flag for cross-validation
;[http://www.ccp4.ac.uk/dist/html/freerunique.html freerunique] : convert FreeRflags between CCP4 and other formats (see freerflag, uniqueify, mtz2various, f2mtz)
;[http://www.ccp4.ac.uk/dist/html/mtz2various.html mtz2various] : produces reflexion file for MULTAN, SHELX, TNT, X-PLOR/CNS, pseudo-SCALEPACK, XtalView, mmCIF or other ascii format
;[http://www.ccp4.ac.uk/dist/html/mtzdump.html mtzdump] : dump data from an MTZ reflection data file
;[http://www.ccp4.ac.uk/dist/html/mtzMADmod.html mtzMADmod] : Generate F+/F- or F/D from other for anomalous data
;[http://www.ccp4.ac.uk/dist/html/mtzmnf.html mtzmnf] : Identify missing data entries in an MTZ file and replace with a Missing Number Flag (MNF)
;[http://www.ccp4.ac.uk/dist/html/mtztona4.html mtztona4] : interconvert MTZ reflection file and ASCII format
;[http://www.ccp4.ac.uk/dist/html/mtzutils.html mtzutils] : Reflection data files utility program
;[http://www.ccp4.ac.uk/dist/html/sftools.html sftools] : reflection data file utility program
;[http://www.ccp4.ac.uk/dist/html/sortmtz.html sortmtz] : Sort a MTZ reflection data file
;[http://www.ccp4.ac.uk/dist/html/xdldataman.html xdldataman] : manipulation, analysis and reformatting of reflection files (X-windows tool)

==Multiple isomorphous replacement==

;[http://www.ccp4.ac.uk/dist/html/abs.html abs] : determine the absolute configuration (hand) of the heavy atom substructure
;[http://www.ccp4.ac.uk/dist/html/bp3.html bp3] : multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
;[http://www.ccp4.ac.uk/dist/html/findncs.html findncs] : detect NCS operations automatically from heavy atom sites
;[http://www.ccp4.ac.uk/dist/html/mlphare.html mlphare] : maximum likelihood heavy atom refinement and phase calculation
;[http://www.ccp4.ac.uk/dist/html/oasis.html oasis] : A program for breaking phase ambiguity in OAS or SIR
;[http://www.ccp4.ac.uk/dist/html/peakmax.html peakmax] : search for peaks in the electron density map
;[http://www.ccp4.ac.uk/dist/html/rsps.html rsps] : heavy atom positions from derivative difference Patterson maps
;[http://www.ccp4.ac.uk/dist/html/sapi.html sapi] : heavy atom site location
;[http://www.ccp4.ac.uk/dist/html/vecref.html vecref] : Vector-space refinement of heavy atom sites in isomorphous derivatives
;[http://www.ccp4.ac.uk/dist/html/vecsum.html vecsum] : program to deconvolute a Patterson function and solve the structure (unsupported)
;[http://www.ccp4.ac.uk/dist/html/vectors.html vectors] : generates Patterson vectors from atomic coordinates

==Multiwavelength anomalous dispersion (MAD)==

;[http://www.ccp4.ac.uk/dist/html/abs.html abs] : determine the absolute configuration (hand) of the heavy atom substructure
;[http://www.ccp4.ac.uk/dist/html/bp3.html bp3] : multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
;[http://www.ccp4.ac.uk/dist/html/crossec.html crossec] : interpolate X-ray cross sections and compute anomalous scattering factors
;[http://www.ccp4.ac.uk/dist/html/mlphare.html mlphare] : maximum likelihood heavy atom refinement and phase calculation
;[http://www.ccp4.ac.uk/dist/html/oasis.html oasis] : A program for breaking phase ambiguity in OAS or SIR
;[http://www.ccp4.ac.uk/dist/html/revise.html revise] : estimates optimised value of the normalised anomalous scattering using MAD data
;[http://www.ccp4.ac.uk/dist/html/sapi.html sapi] : heavy atom site location

==Native protein data at atomic resolution==

;[http://www.ccp4.ac.uk/dist/html/acorn.html acorn] : Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure

==Others / jiffies==

;[http://www.ccp4.ac.uk/dist/html/phistats.html phistats] : Analysis of agreement between phase sets, and checking it against weighting factors
;[http://www.ccp4.ac.uk/dist/html/stereo.html stereo] : Extract coordinates from stereo diagrams
;[http://www.ccp4.ac.uk/dist/html/stgrid.html stgrid] : Generate plot to measure angular coordinates on a stereographic projection from polarrfn
;[http://www.ccp4.ac.uk/dist/html/stnet.html stnet] : Generate plot to measure angles between points on a stereographic projection from polarrfn
;[http://www.ccp4.ac.uk/dist/html/tracer.html tracer] : Lattice TRAnsformation and CEll Reduction

==Plotting / graphics==

;[http://www.ccp4.ac.uk/dist/html/astexviewer.html astexviewer] : Java program for display molecular structures and electron density maps
;[http://www.ccp4.ac.uk/dist/html/ccp4mapwish.html ccp4mapwish] : custom wish interpreter required for MapSlicer
;[http://www.ccp4.ac.uk/dist/html/hklplot.html hklplot] : plots a precession photo from an HKL data file
;[http://www.ccp4.ac.uk/dist/html/hklview.html hklview] : displays zones of reciprocal space as pseudo-precession images (X-windows program)
;[http://www.ccp4.ac.uk/dist/html/ipdisp.html ipdisp] : displays images from a variety of (crystallographic) sources (X-Windows tool)
;[http://www.ccp4.ac.uk/dist/html/loggraph.html loggraph] : viewer for CCP4 formatted `log' files
;[http://www.ccp4.ac.uk/dist/html/mapslicer.html mapslicer] : interactive section viewer for CCP4 map files
;[http://www.ccp4.ac.uk/dist/html/npo.html npo] : Molecule and map plotting
;[http://www.ccp4.ac.uk/dist/html/pltdev.html pltdev] : convert Plot84 meta-files to PostScript, Tektronix or HPGL
;[http://www.ccp4.ac.uk/dist/html/rasmol.html rasmol] : Molecular Visualisation Program (X-windows tool)
;[http://www.ccp4.ac.uk/dist/html/topdraw.html topdraw] : Sketchpad for protein topology diagrams (supported)
;[http://www.ccp4.ac.uk/dist/html/xloggraph.html xloggraph] : a viewer of specially formatted `log' files (X-windows tool)
;[http://www.ccp4.ac.uk/dist/html/xplot84driver.html xplot84driver] : a viewer for Plot84 meta files (X-windows tool)

==Protein sequence file manipulations==

;[http://www.ccp4.ac.uk/dist/html/clustalw.html clustalw interface] : Graphical Interface to the ClustalW Program
;[http://www.ccp4.ac.uk/dist/html/get_prot.html import/edit protein sequence] : Import and edit protein sequences

==Scaling data==

;[http://www.ccp4.ac.uk/dist/html/fhscal.html fhscal] : Scaling of isomorphous derivative data using Kraut's method (see also SCALEIT)
;[http://www.ccp4.ac.uk/dist/html/icoefl.html icoefl] : vectorially combined scaling of Fobs (Iobs) with partial Fc's
;[http://www.ccp4.ac.uk/dist/html/rstats.html rstats] : scale together two sets of F's
;[http://www.ccp4.ac.uk/dist/html/scalechoose.html scalechoose] : information about choice of scaling program (see reindex)
;[http://www.ccp4.ac.uk/dist/html/scaleit.html scaleit] : derivative to native scaling (see also FHSCAL)

==Validation and deposition==

;[http://www.ccp4.ac.uk/dist/html/dhm_tool.html data harvesting manager] : Tool for managing Data Harvesting Files
;[http://www.ccp4.ac.uk/dist/html/pdb_extract.html pdb_extract] : RCSB/PDB Programs for extracting harvest information from program log files

==References==
*Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". ''Acta Cryst, D50:760-763''.

[[Category:ccp4| ]]