Import reflection data in any format, report on contents and create CCP4i2 data objects

Enter a sequence from a sequence file, from a PDB, or by cut and paste

Enter an alignment from a file or by cut and paste

Harvest merged and unmerged files from selected XIA2 data reduction protocols

Select (potentially complicated) subset from a coordinate set

Provide list of chain sequences- import sequence or from coordinate file

Select groups of columns from the MTZ file (csplitmtz)

Select a directory containing images and integrate them

Select a directory containing images and integrate them

Launch iMosflm and capture output

Scale and analyse unmerged data and suggest space group (Pointless, Aimless, Ctruncate, FreeRflag)

Generate a Free R set for a complete set of reflection indices to a given resolution (FreeRflag)

Estimate number of molecules in the asymmetric unit and solvent content (Matthews_coeff)

Evaluate data for anisotropy, optical resolution, pseudo translation and perform self-rotation function (Molrep)

CRANK2 experimental phasing pipeline

Experimental phasing pipeline SHELX (run via Crank2)

Complete a heavy atom model and calculate phases

Un-biased improvement of initial phases for high resolution data (1.5 Angstoms and better)

Modify the electron density (Parrot)

Identify MR models with MrBUMP, display and select with CCP4mg

Use CCP4mg to select components of a search model and output to i2 for MR

Truncate and renumber model prior to molecular replacement

Truncate model prior to molecular replacement

Compile assorted related structures into an ensemble for use in PHASER

Align sequences using clustalw

Run a quick MrBUMP job with streamlined settings

Simple MR with optional refinement and rebuilding (Phaser)

Advanced MR options followed by refinement and rebuilding (Phaser, Refmac5, Coot)

Molecular replacement (Molrep)

Use electron density as the search model (Molrep)

Match symmetry and origin of output model to reference structure (Csymmatch)

Modify the electron density (Parrot)

Iterations of model building (Buccaneer) and refinement (Refmac5, Prosmart and Coot)

Interactive building (Coot)

Use scripts to fit sidechains, perform stepped refinement, fill and fit... (non-interactive Coot)

Find and filter waters based on electron density and contacts (non-interactive Coot)

Build model (ARP/wARP classic)

Interactive molecular graphics: visualization, figure preparation, analysis.

Use Shelxe to attempt to improve (or verify) a solution from Molecular Replacement

Refine (Refmac5) with optional restraints (Prosmart)

Enter TLS information to be used later in the project

Define rigid bodies for refinement (Phaser), fill partial residues (Coot) and refine (Refmac)

Generate a PDB file and dictionary (acedrg) from MOL file, SMILES, or sketch (lidia)

A ligand workflow, starting from merged or unmerged reflections, SMILES, and an isomorphous parent structure

Calculates real-space metrics for evaluating the agreement between model and density (Edstats, cfft)

Interface and assembly analysis (qtpisa)

Checks stereochemistry, conformation and fit to positive omit density, and describes glycans (Privateer)

Calculate mean B-factors, Ramachandran plots and other metrics to aid in validation (Clipper)

Prepare files for deposition

Export 'old' style MTZ file

Reindex to match reference data/coordinates and/or change space group of reflections or Free R set (Pointless)

Calculate anomalous LLG map phased by coordinates to highlight anomalous scatterers (Phaser)

Compute map coefficients from set of observations and phases (cmapcoeff)

Interconvert phases between Hendrickson Lattman and Phi/FOM representation

Compare phases from different sources (with option change of origin/hand)

Convert reflection intensities to structure factors (ctruncate)

Generate a Free R set for a complete set of reflection indices to a given resolution (FreeRflag)

Estimate number of molecules in the asymmetric unit and solvent content (Matthews_coeff)

Match symmetry and origin of output model to reference structure (Csymmatch)

Superpose one protein structure on another

Select (potentially complicated) subset from a coordinate set

Edit PDB/CIF files by hand with the PdbView program

Build an MTZ file from data objects

Exercise CCP4i2 Observed data representation conversions