CCP4 web logo CCP4i: Graphical User Interface
Program List

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Programs/tasks currently implemented in the CCP4 Interface are:

ProgramTaskModuleComment
Acorn Acorn - ab initio Phasing Experimental Phasing See ACORN
AMoRe AMoRe Molecular Replacement See AMoRe
Anisoanl Analyse anisotropic U parameters Refinement See ANISOANL
AreaIMol Accessible Surface Area Calculations Structure Analysis See AREAIMOL
ARP/wARP ARP/wARP Program List See ARP or go to ARP/wARP Home Page
AstexViewer AstexViewer Program List See AstexViewer
Baverage Temperature Factor Analysis Structure Analysis See BAVERAGE
Cad Merge MTZ Files (Cad) Reflection Data Utilities Task also in Experimental Phasing module.
Program also part of "Convert to MTZ & Standardise" Task. See CAD
Combat Import Unscaled Data Data Reduction See COMBAT
Coordconv Convert Coordinate Formats Coordinate Utilities See COORDCONV
Detwin Treat Twinned Data Data Reduction See DETWIN
Distang Build AMoRe Output Model Molecular Replacement See DISTANG
dm Run DM Density Improvement See Kevin's dm Workshop
Dtrek2mtz Import Scaled Data Data Reduction See d*TREK2MTZ and the d*TREK program documentation
Ecalc Prepare Data for HA Search Experimental Phasing Combined with REVISE and MTZ2VARIOUS to prepare data for experimental phasing. See ECALC
Extend Run FFT Several Hidden program. See Extend
F2mtz Convert to MTZ & Standardise Reflection Data Utilities Task also called "Import". See F2MTZ
FFFear FFFear - Fragment Searching Model Building Output coordinates should be seen as Calpha-trace; external model building necessary. See FFFEAR
FFJoin FFJoin - Merge fragments Model Building Output Calpha-trace to be built upon externally. See FFJOIN
FFT Run FFT - Create Map Map & Mask Utilities Generate map with FFT, optionally Extend to cover molecule, convert to alternative format. See FFT
FFT for Patterson Generate Patterson Map Experimental Phasing Run FFT to generate Patterson map, generate 2D plot of Harker sections. See FFT
FFT for native Patterson Analyse Data for MR Molecular Replacement Run FFT to generate native Patterson map to check for pseudo-translation. See FFT
Fhscal Scale and Analyse Datasets Experimental Phasing Choose between FHSCAL and SCALEIT, see scaling. See also FHSCAL
Freerflag Convert to MTZ & Standardise Reflection Data Utilities Task also called "Import", see FreerUnique. See also FREERFLAG
Lsqkab Superpose Molecules Coordinate Utilities Alternative to Top. See LSQKAB
Mapman Run FFT - Create Map Map & Mask Utilities Hidden Program. Non-CCP4; see Uppsala Software Factory - MAPMAN Manual
Mapmask Edit/Rotate Maps & Masks Map & Mask Utilities See MAPMASK
Mapmask Run FFT - Create Map Map & Mask Utilities Hidden Program. Extend map to cover molecule. See MAPMASK
Mapmask Generate Patterson Map Experimental Phasing Hidden program. Reorder map axes. See MAPMASK
Maprot Map cutting Map & Mask Utilities For cutting out density for Molecular Replacement. See MAPROT
Maprot Map Averaging Map & Mask Utilities For averaging and correlation. See MAPROT
Maprot Edit/Rotate Maps & Masks Map & Mask Utilities For interpolation&rotation. See MAPROT
Matthews_coef Cell Content Analysis Coordinate Utilities Task also in Molecular Replacement module. See MATTHEWS_COEF
Mbkall Run FFT - Create Map Map & Mask Utilities Hidden program.
Mlphare Run Mlphare Experimental Phasing See MLPHARE
Modeller Edit Protein Structure Molecular Replacement Non-CCP4 program. See Sali Lab at The Rockefeller University
Molrep Molrep - auto MR Molecular Replacement See MOLREP
Mosflm Integrate Diffraction Images Data Reduction See MOSFLM
Mtz2various Convert from MTZ Reflection Data Utilities Task also called "Export". See MTZ2VARIOUS
Mtz2various Prepare data for HA Search Experimental Phasing Combined with REVISE and ECALC to prepare data for experimental phasing. See MTZ2VARIOUS
Mtzdmp Hidden program, runs when View button is clicked for MTZ files (see View). See also MTZDUMP
Mtzutils Convert to MTZ & Standardise Reflection Data Utilities Hidden program; task also called "Import". See MTZUTILS
Ncsmask Create/Edit Masks Map & Mask Utilities See NCSMASK
Ncsref NCS Phased Refinement Refinement Combination of 'dm' and REFMAC, with a bit of LSQKAB and maybe more, to have a handle on the start of refinement in the case of NCS being present.
NPO Generate Patterson Map Experimental Phasing See NPO
Oasis Oasis - SAD/SIR phasing Experimental Phasing See OASIS
Overlapmap Map Correlation Map & Mask Utilities Used in conjunction with SFALL to calculate map correlation. See OVERLAPMAP
Pdbset Edit PDB File Coordinate Utilities See PDBSET
Peakmax Generate Patterson Map Experimental Phasing See PEAKMAX
Phistats Phase Analysis (Phistats) Reflection Data Utilities See PHISTATS
Prmap Hidden program, runs when View button is clicked for map files. See PRMAP
Procheck Run SFCHECK&PROCHECK Refinement See PROCHECK
Professs Professs - NCS from HA Experimental Phasing See PROFESSS
Rantan Rantan - Direct Methods Experimental Phasing See RANTAN
Rebatch Sort/Reindex MTZ Files Data Reduction See REBATCH
Refmac5 Run Refmac5 Refinement See REFMAC5
Reindex Sort/Reindex MTZ Files Data Reduction See REINDEX. See also Reindex.
Reindex Reindex Reflections Reflection Data Utilities This is the option to use for 'standard' (i.e. non-multi-record) MTZ files. See REINDEX.
Revise Prepare Data for HA Search Experimental Phasing Combined with ECALC and MTZ2VARIOUS. See REVISE
Rotaprep (now called Combat) Import Unscaled Data Data Reduction Now called COMBAT. See COMBAT
RSPS Real Space Patterson Search Experimental Phasing See RSPS
Scala Scale Experimental Intensities Data Reduction See SCALA
Scaleit Scale Datasets Experimental Phasing Choose between SCALEIT and FHSCAL, see scaling. See also SCALEIT
Scalepack2MTZ Import Scaled Data Data Reduction See Scalepack2MTZ
SFall Create Input SFs from Model Molecular Replacement Combined with ECALC to prepare 'map' for use in molecular replacement. See SFALL
SFall Map Correlation Map & Mask Utilities Combined with Overlapmap. See SFALL
SFall Calculate Fs & Phases Reflection Data Utilities See SFALL
SFCHECK Run Sfcheck & Procheck Refinement See SFCHECK
Sftools Edit MTZ File (Sftools) Reflection Data Utilities See SFTOOLS
Sftools - analysis SF File Analysis Reflection Data Utilities See SFTOOLS
Shelx SHELX - Heavy Atom Search Experimental Phasing Non-CCP4 program. See THE SHELX HOMEPAGE
Sigma-A Sigma-A Reflection Data Utilities See SIGMAA
Solomon Run Solomon Density Improvement Includes option to truncate density. See also SOLOMON
Sortmtz Sort/Reindex MTZ Files Data Reduction See SORTMTZ
Top Superpose Molecules Coordinate Utilities Alternative to LSQKAB. See TOP
Tlsanl Analyse TLS parameters Refinement See TLSANL
Truncate Convert Intensities to SFs Data Reduction Be careful with LABIN/LABOUT. See TRUNCATE. Also part of the 'Import Scaled Data' task.
Uniqueify Convert to MTZ & Standardise Reflection Data Utilities Task also called "Import", see FreerUnique. See also UNIQUE
Vectors Generate Patterson Map Experimental Phasing See VECTORS
warpNtrace Run warpNtrace Model Building Direct from author(s); see ARP-wARP
XtalView/xfit XtalView/xfit Model Building See XtalView
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