Difference between revisions of "List of ccp4 programs"

Latest revision as of 01:27, 29 September 2007

see: CCP4 v6.0.2 Program Documentation

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

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

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

clustalw interface 

Graphical Interface to the ClustalW Program

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

References

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