CCP4 v3.2 Program Documentation

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

General

• ccp4 - introduction to the CCP4 Program Suite under Unix

Supported Programs

• abscale - Reads data from the Generate file produced by MOSFLM, applies corrections
• absurd - for initial processing of intensity files from MADNES
• act - analyse coordinates.
• agrovata - apply scale factors and average data
• almn - calculates rotation function overlap values using FFT techniques
• amore - Jorge Navaza's state-of-the-art molecular replacement package.
• bones2pdb - Make a `.pdb' pseudo-coordinate file from a bones file
• cad - Collect and sort crystallographic reflection data from several files,
• coordconv - Interconvert various coordinate formats
• crossec - interpolate X-ray cross sections and compute anomalous scattering factors
• distang - Distances and angles calculation
• dm - density modification package, release 1.6, 28/7/94
• ecalc - calculate normalised structure amplitudes
• extend - Extend Fourier maps
• f2mtz - Convert a formatted reflection file to mtz format
• fft, fftbig - fast Fourier transform
• fhscal - Scaling of isomorphous derivative data using Kraut's method.
• freerflag - tags each reflection in an MTZ file with a flag for cross-validation
• hgen - generate hydrogen atom positions for proteins
• hklplot - plots a precession photo from an HKL data file
• icoefl - vectorially combined scaling of Fobs (Iobs) with partial Fc's
• lsqkab - apply various transformations to coordinate files.
• makedict - converts PDB file to TNT or PROTIN dictionaries and PROTIN to PDB.
• mama2ccp4 - Convert between `mama' and Cambridge/CCP4 map formats.
• mapmask - map/mask extend program
• maprot - map skewing, interpolating, rotating, averaging and
• maptona4 - Convert binary map file to and from na4 ascii format
• matthews_coef - Misha Isupov's Jiffy to calculate Matthews coefficient.
• mlphare - maximum likelihood heavy atom refinement and phase calculation
• mtz2various - produces reflexion file for MULTAN, SHELX, TNT, X-PLOR or other ascii format.
• mtzdump, mtzdmp - dump data from an MTZ reflection data file
• mtzmnf - Identify missing data entries in an MTZ file and replace with
• mtztona4, na4tomtz - interconvert MTZ reflection file and ASCII format.
• mtzutils - Reflection data files utility program
• ncsmask - averaging mask manipulation program
• npo - Molecule and map plotting
• overlapmap - calculates the average of two maps
• pdbset - various useful manipulations on coordinate files
• phistats - Analysis of agreement between phase sets, and checking it against weighting factors.
• pltdev - convert Plot84 meta-files to PostScript, Tektronix or HPGL.
• polarrfn - fast rotation function which works in polar angles
• polypose - a program for superimposing many multi-domain structures
• prolsq - Hendrickson-Konnert structure refinement
• protin - prepare restraints file for prolsq or refmac.
• reindex - produces an MTZ file with h k l reindexed and/or the symmetry changed,
• rotaprep - produces an MTZ file in multirecord form suitable for input to SCALA, AGROVATA.
• rotavata - calculate scale factors for overlapping batches of data
• rotmat - interconverts CCP4/MERLOT/X-PLOR rotation angles.
• rsearch - R-factor and correlation coefficient between Fcalc and Fobs
• rstats - scale together two sets of F's
• scaleit - derivative to native scaling
• scalepack2mtz - converts merged scalepack output into MTZ format.
• sfall - Structure factor calculation and X-ray refinement using forward and reverse FFT
• sigmaa - Improved Fourier coefficients using calculated phases
• sortmtz - Sort a MTZ reflection data file
• stereo - Extract coordinates from stereo diagrams
• tffc - Translation Function Fourier Coefficients
• tlsanl - evaluate TLS tensors from restrain
• tracer - Lattice TRAnsformation and CEll Reduction
• truncate - Truncate reflection data
• undupl - remove duplicates from Madnes data, after Absurd
• unique - Generate a unique list of reflections
• watertidy - rationalise waters at the end of refinement
• wilson - Wilson plot, absolute scale and temperature factor
• xloggraph - X-windows tool, a viewer of specially formatted `log' files.
• xplot84driver - X-windows tool, a viewer for Plot84 meta files.

Unsupported Programs

• flatmap - use molecular envelope to flatten solvent region of map

Libraries

• mtzlib - Subroutine Library for Reflection data file handling