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# Define the tasks in each interface module
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PROJECT CCP4

TITLE CCP4 Program Interface

MODULE datred  Data Reduction

#  ximage      View Data Image
#  Testing...testing...testing....

  scalepack2mtz  Import Scaled Denzo Data
  Import data from scalepack

  dtrek2mtz	Import Scaled D*trek Data
  Import data from D*trek

  combat Import Unscaled Data
  Run combat to convert various file formats to MTZ

  sortmtz Sort/Reindex MTZ Files
  Sort/Merge/Reindex/Rebatch multi-record MTZ file(s)

  scala Scale Experimental Intensities
  Run Scala to scale experimental intensities

  truncate Convert Intensities to SFs
  Run Truncate program to convert intensities to SFs

  detwin Treat Twinned Data
  Run detwin program to analyse and detwin data

MODULE exptphase Experimental Phasing

  scaleit Scale Datasets
  Run Scaleit or Fhscal to scale derivative and native data

  prephadata Prepare Data for HA Search
  Run Revise/Ecalc/Mtz2various to calc FM/normalise/convert format for RSPS/Rantan/Shelx

  shelx Shelx - Heavy Atom Search
  Use Shelx direct methods or Patterson search to find heavy atoms

  rantan  Rantan - Direct Methods
  Rantan - direct methods to solve heavy atom or small molecule

  patterson Generate Patterson Map
  Run FFT to generate Patterson map, generate 2D plot of Harker sections

  rsps    Real Space Patterson Search
  RSPS Find or test MIR solutions

  mlphare Run Mlphare
  Run Mlphare heavy atom refinement program


MODULE molrepl Molecular Replacement

  mr_analyse  Analyse Data for MR
  Create native Patterson to check for pseudo-translation

  molrep  Molrep - auto MR
  Also self rotation, searching map for molecule.

  mr_map	Create Input SFs from Model
  Use Sfall to generate map (using Fs or E's) from coordinates

  mr_database     AMoRe Model Database
  AMoRe model database

  amore 	AMoRe
  Run AMoRe rotation and translation functions

  mr_edit	Edit AMoRe Solution File
  Edit AMoRe solution file to select solutions to use

  mr_solution	Build AMoRe Output Model
  Generate solution coordinate file, display and analyse solution

  modeller	Edit Protein Structure
  Use Modeller, homology modelling, program to edit protein

MODULE improvement Density Improvement

  dm		Run DM
  Density modification using the DM program

  solomon 	Run Solomon
  Density modification using the Solomon program

  dmmulti	Run DmMulti
  Multi-crystal density modification

MODULE build Model Building

  fffear        FFFear - Fragment Searching
  Search for molecular fragments in poor quality electron density maps

  ffjoin        FFJoin - Merge fragments
  Merge PDB files containing results from different runs of FFFear

  xfit          XtalView/xfit
  Launch XtalView model building+map fitting

MODULE refinement Refinement

  refmac5        Run Refmac5
  Refinement using Refmac 5.0.n

  pdb_restraints Edit Restraints in PDB File
  Edit Restraints in PDB File

  sketch        Monomer Library Sketcher
  Sketch small molecule to create library entry

  ncsref	NCS Phased Refinement
  Use NCS to generate target phases for refinement (using DM & Refmac)

  watertidy     Tidy Waters
  Rationalise waters at the end of refinement

  check		Run Sfcheck & Procheck
  Analysis of structure geometry & fit of structure to experimental data.

MODULE analysis Structure Analysis

  contact Analyse Molecular Contacts
  Analyse contacts in or between protein molecules

  baverage Temperature Factor Analysis
  Plot B-factor versus residue number

MODULE maputils Map & Mask Utilities

  task_maps	Create Task-Specific Maps
  Create the maps from output of previous Refmac/NCS Refinement/Dm/Solomon jobs

  fft           Run FFT - Create Map
  Generate map with FFT, optionally Extend to cover molecule, convert to other map formats

  ncsmask       Create/Edit Masks
  Use Ncsmask to create mask from coordinates and/or cleanup a mask

  maputils       Edit/Rotate Maps & Masks
  Edit maps and masks using Mapmask and Maprot

  mapave        Map Averaging
  Map averaging & correlation maps using Maprot

  map_correl    Map Correlation
  Use Sfall and Overlapmap to find map correlation

MODULE mtz_utils Reflection Data Utilities

  sfall         Calculate Fs & Phases
  Run Sfall to calculate Fs & phases from map or coordinates

  import        Convert to MTZ & Standardise
  Convert hkl file to MTZ(f2mtz) and cleanup mtz file (Uniqueify,Freerflag)

  export        Convert from MTZ
  Convert MTZ to various HKL file formats (Mtz2various)

  sftools        Edit MTZ File (Sftools)
  Use Sftools to edit MTZ file

  cad           Merge MTZ Files (Cad)
  Merge MTZ files

  edit_dname	Edit MTZ Project&Dataset
  Use CAD to change assignment of projects and dataset names

  reindex 	Reindex Reflections
  Use Reindex to reindex reflections & change spacegroup

  sfanal        SF File Analysis
  Sftools analysis and plotting of SF data

  sigmaa        Sigma-A
  Improved Fourier Coefficients using calculated phases

MODULE coord_utils Coordinate Utilities

  matthews      Cell Content Analysis
  Find Matthews coefficient and solvent content

  coordconv	Convert Coordinate Formats
  Convert coordinate file formats

  pdbset	Edit PDB File
  Convert PDB files to form acceptable to most CCP4 programs

  superpose	Superpose Molecules 
  Superpose molecules using Lsqkab or Top


MODULE programlist Program List

#  demo	Task Interface Demo
#  Run the demo task interface

  amore		AMoRe
  Run AMoRe rotation and translation functions

  arp_warp		ARP/wARP
  Refine & find missing atoms

  baverage Baverage
  Plot B-factor versus residue number

  cad		Cad
  Merge or edit MTZ files

  combat        Combat
  Import unscaled data for processing by Scala

  coordconv     Coordconv
  Convert coordinate file formats

  detwin	Detwin
  Analyse and detwin twinned data

  mr_solutions	Distang
  Build and analyse MR solution model

  dm		DM
  Density modification

  dtrek2mtz     Dtrek2mtz
  Import data fom D*trek

  prephadata	Ecalc
  Convert SFs to normalised structure amplitudes

  import	F2mtz (import)
  Convert reflection file to MTZ format

  fffear        FFFear
  Search for molecular fragments in poor quality electron density maps

  ffjoin        FFJoin
  Merge PDB files containing results from different runs of FFFear

  fft		FFT
  Generate map with FFT, optionally Extend to cover molecule, convert to other map formats

  patterson	FFT for Patterson
  Generate Patterson map

  scaleit	Fhscal (scaleit)
  Scale derivative and native data

  import	Freerflag (import)
  Select reflections for FreeR set

  superpose	Lsqkab (superpose)
  Superpose molecules

  fft		Mapman (fft)
  Convert map to O format

  maputils       Mapmask
  Map and mask utilities

  fft		Mapmask (fft)
  Extend map to cover molecule

  patterson	Mapmask (patterson)
  Reorder map axes

  mapave	Maprot (for averaging)
  Use Maprot for correlation maps and map averaging

  maputils	Maprot (Interpolation & rotation)
  Use Maprot for map interpolation and rotation

  matthews      Matthews_coef
  Find Matthews coefficient and solvent content

  fft		Mbkall (fft)
  Convert map to Quanta format

  mlphare	Mlphare
  Refine heavy atom positions

  modeller      Modeller
  Use Modeller, homology modelling, program to edit protein

  molrep	Molrep
  Molecular Replacement & self-rotation

  export	Mtz2various (export)
  Convert MTZ file to various reflection file formats

  ncsmask	Ncsmask
  Create mask from coordinates and/or cleanup a mask

  patterson	NPO (patterson)
  Plot map sections and optionally atoms on section

  map_correl	Overlapmap
  Find map correlation

  pdbset        Pdbset
  Edit PDB File

  patterson	Peakmax (patterson)
  Find peaks in a map

  check         Procheck
  Analysis of structure geometry

  protin        Setup Protin
  Use Protin to set up restraints for Refmac

  rantan	Rantan
  Rantan - direct methods to solve heavy atom or small molecule

  sortmtz	Rebatch
  Edit batch numbers in multi-record MTZ files

  refmac	Run 'old' Refmac
  Refine molecule geometry 

  refmac5	Refmac5
  Refine molecule geometry 

  reindex	Reindex
  Reindex MTZ file(s)

  prephadata	Revise
  Estimate FM for MAD data

  combat	Rotaprep (now called Combat)
  Import unscaled data for processing by Scala

  rsps		RSPS
  Real Space Patterson Search

  scala		Scala
  Scale intensity data

  scaleit	Scaleit
  Scale derivative and native data

  scalepack2mtz  Scalepack2mtz
  Import data from scalepack

  sfcheck       Sfcheck 
  Analysis of fit of structure to experimental data.

  sfall         SFall
  Run Sfall to calculate Fs & phases from coordinates or map

  sftools	Sftools
  Use Sftools to edit MTZ file

  shelx		Shelx
  Use direct methods to find heavy atoms

  sigmaa        Sigma-A
  Improved Fourier Coefficients using calculated phases

  solomon	Solomon
  Density Modification

  sortmtz	Sortmtz 
  Sort/Merge multi-record MTZ file(s)

  superpose	Top
  Superpose protein topology

  truncate	Truncate
  Convert intensities to SFs

  import	Uniqueify (import)
  Generate full unique set of reflections

  patterson	Vectors (patterson)
  Calculate vectors in Patterson maps

  xfit          XtalView/xfit
  Launch XtalView model building+map fitting

