Wikiomics:Crystallography toolbox

Crystallography toolbox

Data integration

• denzo) (from HKL)
• mosflm (from ccp4)
• d*TREK
• XDS

Scaling

• scalepack (from HKL)
• scala (from ccp4)
• xprep (from xprep/Bruker)
• XSCALE

Phasing

Molecular replacement

• MolRep (from ccp4)
• Beast (from ccp4)
• AMoRe (from ccp4)
• Phaser (from ccp4)
• EPMR
• Queen of Spades
• COMPANG
• BRUTEPTF (phased molecular replacement)

Heavy atom methods

Patterson methods

• SOLVE
• fft (from ccp4)
• xHercules (from xtalview)

Direct and dual-space methods

• SHELX-D from shelex
• Shake and Bake (SnB)
• Rantan (from ccp4)

Ab initio methods

• Acorn (from ccp4)
• Oasis (from ccp4)

Phase refinement

• SHARP/autoSHARP SHARP suite
• Mlphare, Vecref (from ccp4)
• Resolve
• SHELX-E
• DM (from ccp4)
• Dmmulti (from ccp4)
• SOLOMON (from ccp4)

Model building

• Automated model building
  • Resolve
  • ARP/wARP (from ccp4) http://www.embl-hamburg.de/ARP/
  • Fffear, ffjoin (from ccp4)
• Interactive model building
  • O (from Uppsala Software Factory)
  • coot
  • Quanta [1]
  • Xtalview
  • Turbo Frodo

Model refinement

• CNS
• refmac (from ccp4)
• TNT

Structure validation

• Procheck Procheck
• WhatIf

Utilities

• Uppsala Software Factory (USF) [2]
• ccp4

Credits

• Tina Bakolitsa wrote this list
• Darek Kedra translated it into wiki and added links