CCP4i2 Task Documentation
data_entry

Import merged data, sequences, alignments or coordinates

import_merged

Import merged reflection data

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

ProvideSequence

Import a sequence

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

ProvideAlignment

Import an alignment

Enter an alignment from a file or by cut and paste

AlternativeImportXIA2

Import Xia2 results

Harvest merged and unmerged files from selected XIA2 data reduction protocols

coordinate_selector

Import a coordinate set - optional selection of subset

Select (potentially complicated) subset from a coordinate set

data_processing

Integrate X-ray images

simple_xia2

Automated integration of images with DIALS - XIA2

Select a directory containing images and integrate them

imosflm

Integrate images with Mosflm

Launch iMosflm and capture output

data_reduction

X-ray data reduction and analysis

aimless_pipe

Data reduction - AIMLESS

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

freerflag

Generate a Free R set

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

matthews

Estimate cell content

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

molrep_selfrot

Calculate self rotation function

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

expt_phasing

Experimental phasing

crank2

Automated structure solution - CRANK2

CRANK2 experimental phasing pipeline

shelx

Automated structure solution - SHELXC/D/E

Experimental phasing pipeline SHELX (run via Crank2)

phaser_EP_AUTO

SAD phasing from heavy atom sites - PHASER

Complete a heavy atom model and calculate phases

parrot

Density modification - PARROT

Modify the electron density (Parrot)

ShelxCD

Find HA sites - SHELXC/D

Find sites from SAD/MAD/SIR/SIRAS/RIP/RIPAS data

ShelxCECompareHands

ShelxE Compare hands pipeline

Phasing, density modification and autobuilding - both hands of the HA structure

bioinformatics

Bioinformatics and model preparation for Molecular Replacement

ccp4mg_edit_model

Interactive model preparation - CCP4mg and MrBUMP

Edit molecular replacement search models (ccp4mg)

chainsaw

Truncate search model - CHAINSAW

Truncate and renumber model prior to molecular replacement

sculptor

Truncate search model - SCULPTOR

Truncate model prior to molecular replacement

clustalw

Align sequences - CLUSTALW

Align sequences using clustalw

molecular_replacement

Molecular Replacement

mrbump_basic

Automated structure solution - MrBUMP

Run a quick MrBUMP job with streamlined settings

phaser_pipeline

Molecular Replacement and refinement - PHASER

Molecular replacement followed by refinement and rebuilding (Phaser, Refmac, Coot)

molrep_pipe

Molecular Replacement and refinement - MOLREP

Molecular replacement (Molrep)

molrep_den

Molecular replacement with electron density - MOLREP

Use electron density as the search model (Molrep)

csymmatch

Match model to reference structure

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

parrot

Density modification - PARROT

Modify the electron density (Parrot)

model_building

Model building and Graphics

buccaneer_build_refine_mr

Autobuild protein - BUCCANEER

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

coot_rebuild

Manual model building - COOT

Interactive building (Coot)

coot_script_lines

Scripted model building - COOT

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

coot_find_waters

Find waters - COOT

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

arp_warp_classic

ARP/wARP

Build model (ARP/wARP classic)

ccp4mg_general

Molecular graphics visualization and figure creation - CCP4MG

Interactive molecular graphics: visualization, figure preparation, analysis.

refinement

Refinement

prosmart_refmac

Refinement - REFMAC5

Refine (Refmac5) with optional restraints (Prosmart)

ProvideTLS

Import and/or edit TLS set definitions

Enter TLS information to be used later in the project

phaser_rnp_pipeline

Rigid body refinement - PHASER

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

ligands

Ligands

LidiaAcedrg

Make Ligand

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

SubstituteLigand

Automated solution of isomorphous ligand complex

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

validation

Validation and analysis

edstats

Analyse agreement between model and density - EDSTATS

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

privateer_validate

Validation of carbohydrate structures - PRIVATEER

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

qtpisa

Interface and quaternary structure analysis - PISA

Interface and assembly analysis (qtpisa)

validate_protein

Analyse model geometry

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

export

Export and Deposition

PrepareDeposit

Prepare files for deposition

Prepare files for deposition

mergeMtz

Merge experimental data objects to MTZ

Export 'old' style MTZ file

expt_data_utility

Reflection data tools

pointless_reindexToMatch

Reindex or change spacegroup

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

phaser_EP_LLG

Anomalous map from coordinates - PHASER

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

cmapcoeff

Calculate unusual map coefficients

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

chltofom

Convert HL phase to and from Phi/Fom

Interconvert phases between Hendrickson Lattman and Phi/FOM representation

cphasematch

Match and analyse phases to reference set

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

ctruncate

Convert intensities to amplitudes

Convert reflection intensities to structure factors (ctruncate)

splitMtz

Split MTZ into experimental data objects

Select groups of columns from the MTZ file (csplitmtz)

freerflag

Generate a Free R set

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

matthews

Estimate cell content

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

model_data_utility

Coordinate data tools

csymmatch

Match model to reference structure

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

gesamt

Structural alignment - Gesamt

Superpose one protein structure on another

coordinate_selector

Import a coordinate set - optional selection of subset

Select (potentially complicated) subset from a coordinate set

pdbview_edit

Edit PDB/CIF files by hand

Edit PDB/CIF files by hand with the PdbView program

developer_tools

Developer tools

MakeMonster

Export monster mtz

Build an MTZ file from data objects

TestObsConversions

Test CCP4i2 observed data interconversions

Exercise CCP4i2 Observed data representation conversions