CCP4i2 Task Documentation

Import merged data, AU Contents, alignments or coordinates

• Import merged
• Define AU contents
• Import sequence or alignment
• Import alignment
• Import XIA2 results
• Import or select subset from coordinate set
• splitMtz
• import_serial

Integrate X-ray images

• Xia2 with DIALS
• Xia2 with XDS
• Integrate images with iMosflm
• DIALS Image Viewer
• DIALS Reciprocal Lattice Viewer
• Integrate images with DIALS - using DUI

X-ray data reduction and analysis

• Aimless data reduction pipeline
• Generate a Free R set
• Estimate AU content
• Self-Rotation Function Analysis with Molrep
• AUSPEX

AlphaFold and RoseTTAFold Utilities

• Use CCP4MG to edit a model
• MrParse: Finding search models in the PDB and the EBI Alphafold database
• Process Predicted Models
• MR with model splitting using Slice-n-Dice
• Ab initio phasing and chain tracing - ARCIMBOLDO

Experimental phasing

• Crank2 experimental phasing task
• SHELXC/D/E experimental phasing task
• SAD phasing with Phaser

Use fprime to calculates anomalous scattering factors (f’ and f”) if needed

Bioinformatics

• Use CCP4MG to edit a model
• CCP4MG Edit Search Model
• Truncate Search Model
• Truncate search model - SCULPTOR
• Build an ensemble for Phaser
• Align sequences - CLUSTALW
• MrParse: Finding search models in the PDB and the EBI Alphafold database
• FindMySequence

Molecular replacement

• Automated Molecular Replacement from target sequence
• Use Phaser to carry out molecular replacement
• Molecular replacement - MOLREP
• SYMMETRY MATCH MODEL TO REFERENCE
• Molecular Replacement with unconventional model – AMPLE
• Molecular replacement with fragments (Fragon)
• Calculate omit map
• DIMPLE
• Morda Installation
• Single atom Molecular Replacement

Density Modification

• Density Modification using Acorn
• Density Modification (parrot)

Model building and graphics

• Autobuild protein (buccaneer)
• Model Building with ARP/wARP
• ModelCraft
• Manual model rebuilding
• Find waters with COOT
• Coot Scripting from CCP4i2
• Autobuild RNA (nautilus)
• Molecular graphics vizualization and figure creation - CCP4MG
• Using SHELXE for Molecular Replacement
• Data reduction, molecular replacement and model building pipeline

Refinement

• Refinement
• TLS
• Real space refinement morphing with COOT
• Low Resolution Structure Refinement Pipeline
• PAIREF
• Shift field refinement

Ligands

• Make Ligand Coordinate and Restraint Dictionaries with Acedrg

Valiation and analysis

• Validate protein geometry (clipper)
• Analyse agreement between model and density (edstats)
• Validation of carbohydrate structures (Privateer)
• Structure analysis with PISA
• Space Group Validation with Zanuda

Export and Deposition

• Prepare and validate files for deposition
• Merge experimental data objects to MTZ

Reflection data tools

• Reindex or change spacegroup
• Phase comparison (cphasematch)
• Calculate unusual map coefficients (cmapcoeff)
• Intensities to amplitudes
• Convert between Hendrickson-Lattman coefficients and phi/FOM
• Generate a Free R set
• Estimate AU content

Coordinate data tools

• Structure alignment using gesamt
• Import or select subset from coordinate set
• Add Fractional Coordinates

Indices and tables

• Index

• Module Index

• Search Page