Category:Ccp4

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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.

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

See also

External links

Pages in category "Ccp4"

The following 7 pages are in this category, out of 7 total.