Wikiomics:Crystallography toolbox

Crystallography toolbox

Data integration

• denzo (from HKL [1])
• mosflm (from ccp4 [2])
• d*TREK [3]
• XDS [4]

Scaling

• scalepack (from HKL)
• scala (from ccp4)
• xprep (from xprep/Bruker)
• XSCALE [5]

Phasing

Molecular replacement

• MolRep (from ccp4)
• Beast (from ccp4)
• AMoRe (from ccp4)
• Phaser (from ccp4)
• EPMR [6]
• Queen of Spades [7]
• COMPANG [8]
• BRUTEPTF (phased molecular replacement, http://russel.bioc.aecom.yu.edu/server/NYSGRC.html)

Heavy atom methods

Patterson methods

• SOLVE [9]
• fft (from ccp4)
• xHercules (from xtalview [10])

Direct and dual-space methods

• SHELX-D [from shelex http://shelx.uni-ac.gwdg.de/SHELX/]
• Shake and Bake (SnB) [11]
• Rantan (from ccp4)

Ab initio methods

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

Phase refinement

• SHARP/autoSHARP (SHARP suite [12])
• Mlphare, Vecref (from ccp4)
• Resolve http://www.solve.lanl.gov/
• 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) [13]
  • coot [http://www.ysbl.york.ac.uk/~emsley/coot/
  • Quanta [14]
  • Xtalview
  • Turbo Frodo [15]

Model refinement

• CNS [16]
• refmac (from ccp4)
• TNT [17]

Structure validation

• Procheck [18]
• WhatIf [19]

Utilities

• Uppsala Software Factory (USF) [20]
• ccp4

Credits

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