List of ccp4 programs
From Christoph's Personal Wiki
The Collaborative Computational Project Number 4 in protein crystallography or (CCP4) was set up in 1979 in the United Kingdom to support collaboration between researchers software development and assemble a comprehensive collection of software for structural biology.
Contents
- 1 List of programs
- 1.1 Coordinate file manipulations
- 1.2 Data harvesting and datasets
- 1.3 Data processing and reduction
- 1.4 Density fitting and model building
- 1.5 Density modification : molecular averaging
- 1.6 Experimental phasing
- 1.7 Map calculation and manipulation
- 1.8 Model analysis
- 1.9 Model refinement
- 1.10 Molecular replacement
- 1.11 MTZ manipulations / conversions=
- 1.12 Multiple isomorphous replacement
- 1.13 Multiwavelength anomalous dispersion (MAD)
- 1.14 Native protein data at atomic resolution
- 1.15 Others / jiffies
- 1.16 Plotting / graphics
- 1.17 Protein sequence file manipulations
- 1.18 Scaling data
- 1.19 Validation and deposition
List of programs
Coordinate file manipulations
- bones2pdb
- Make a PDB pseudo-coordinate file from a bones file
- chainsaw
- Mutate a pdb file according to an input sequence alignment
- interface.html 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
- pdb_merge
- merge two coordinate files into one
- pdbset
- various useful manipulations on coordinate files
- reforigin
- apply best origin shift to PDB atom co-ords according to reference file (unsupported)
- rwcontents
- Count atoms by type
- sortwater
- sort waters by the protein chain to which they "belong"
- superpose
- structural alignment based on secondary structure matching
- 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
- arp_waters
- Automated Refinement Procedure for refining protein structures
- fragment library.html fffear fragment library
- map interpretation package
- fffear
- map interpretation package
- ffjoin
- joining model fragments from FFFEAR
Density modification : molecular averaging
- hltofom
- Convert to/from Hendrickson-Lattman coefficients
- pirate
- Statistical Phase Improvement
- 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
Experimental phasing
- acorn
- Molecular Replacement, Sayre Equation and Dynamic Density Modification for the determination of a protein structure
- crank
- Automated structure solution for experimental phasing
- rantan
- Direct Method module for the determination of heavy atom positions
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
- table.html 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
- phaser
- Maximum Likelihood Phasing
- 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
- bp3
- multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
- 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 (MAD)
- abs
- determine the absolute configuration (hand) of the heavy atom substructure
- bp3
- multivariate likelihood substructure refinement and phasing of S/MIR(AS) and/or S/MAD
- 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
- 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
- interface.html clustalw interface
- Graphical Interface to the ClustalW Program
- protein sequence.html import/edit protein sequence
- Import and edit protein sequences
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
- data harvesting manager
- Tool for managing Data Harvesting Files
- pdb_extract
- RCSB/PDB Programs for extracting harvest information from program log files
