CCP4 school: Tutorials

CCP4wiki

For up-to-date documentation on all of CCP4's software and lots of other useful information for X-ray crystallographers see the CCP4 Wiki.

CCP4 Webservices - Balbes, etc..

Webservices from CCP4 online, UK. Services include BALBES, MrBUMP, ZANUDA, PISA CCP4 Webservices.

2017 Lecture Notes and Tutorial Material

• iMosflm training
• Mosflm examples

2014 Lecture Notes and Tutorial Material

• Introduction
• The diffraction experiment (P.Evans)
• Data reduction (P.Evans)
• Tutorial - iMosflm
• Tutorial - iMosflm advanced
• Data collection strategy (P.Evans)
• SHELX suite (R.Pannu)
• Crank experimental phasing (R.Pannu)
• Tutorial - Crank
• Tutorial -shelx
• Molecular replacement (A.Lebedev)
• Automatic MR in ccp4 (G.Murshudov)
• Introduction to Coot (B.Lohkamp)
• Density Modification (R.Pannu)
• Tutorial - basic MR and phasing
• Refinement (G.Murshudov)
• Monomer dictionary (G.Murshudov)
• Model building with buccaneer (B.Lohkamp)
• ARP/wARP model building (J.Pereira)
• Tutorial -ARP/wARP
• More coot and ligands (B.Lohkamp)
• ARP/wARP ligands (J.Pereira)
• Zanuda and data pathologies (A.Lebedev)
• Oligomers (E.Krissinel)

• 2012 Lecture Notes and Tutorial Material

  Data Collection and Processing

  Phil Evans

  Lecture Notes:

  • Data reduction (pdf)
  • Diffraction geometry and integration (pdf)

  Twinning

  Andrea Thorn

  Lecture Notes:

  • Twinning (pdf)

  CCP4 MR pipelines

  Charles Ballard

  Lecture Notes:

  • MR pipelines (pdf)

  Phaser MR

  Gabor Bunkozci

  Lecture Notes:

  • Phaser MR (pdf)

  Introduction to coot

  Paul Emsley

  Lecture Notes:

  • COOT: the basics (pdf)
  • Coot tutorial data

  Experimental phasing with SHELX

  Andrea Thorn

  Lecture Notes:

  • shelx (pdf)

  Experimental phasing with CRANK

  Raj Pannu

  Lecture Notes:

  • CRANK experimental phasing (pdf)

  MR-SAD

  Gabor Bunkozci

  Lecture Notes:

  • Phaser Experimental phasing and MR-SAD (pdf)
  • Phaser EP tutorial (pdf)

  Density ModificationK

  Raj Pannu

  Lecture Notes:

  • Density modification (pdf)

  Refinement with Refmac

  Garib Murshudov

  Lecture Notes:

  • Refmac (pdf)

  Refmac dictionary

  Garib Murshudov

  Lecture Notes:

  • Refmac dictionary (pdf)

  ARPwARP model building

  Tim Wiegels

  Lecture Notes:

  • ARPwARP (pdf)

  ARPwARP ligands

  Ciaran Carolan

  Lecture Notes:

  • ARPwARP ligands(pdf)

  PISA

  Eugene Krissnel

  Lecture Notes:

  • PISA (pdf)

  The PDBj

  Nobutoshi Itoh

  Lecture Notes:

  • PDBj (pdf)

  2011 Lecture Notes and Tutorial Material

  Data Collection and Processing

  Phil Evans

  Lecture Notes:

  • Data reduction (pdf)
  • Diffraction geometry and integration (pdf)

  Experimental Phasing and Density Modification

  Pavol Skubak, Charles Ballard

  Lecture Notes:

  • Experimental Phasing with Phaser (pdf)
  • Density Modification (pdf)
  • Experimental Phasing with Crank (pdf)

  Molecular Replacement

  Garib Murshudov, Ronan Keegan

  Lecture Notes:

  • Introduction to Molecular Replacement (pdf)
  • Molecular Replacement with Phaser (pdf)
  • MrBUMP - Automated Molecular Replacement (pdf)
  • Balbes (pdf)

  Tutorial Material:

  • CCP4 Molecular Replacement and MrBUMP Tutorial (Basic)
  • CCP4 Molecular Replacement and MrBUMP Tutorial (Advanced)

  Model Building: Coot & Buccaneer

  Bernhard Lohkamp

  Lecture Notes:

  • Coot:
    • Model Building with Coot - An Introduction (pdf)
    • Model Building with Coot - Secondary Structure Tools (pdf)
    • Ligand Building and Structure Validation in Coot (pdf)
  • Buccaneer:
    • Automated Model Building with Buccaneer (pdf)

  Tutorial Material:

  • Coot Crib Sheet (pdf)
  • Coot Tutorial 1 (pdf)
  • Coot Tutorial 2 (pdf)

  Shelx and Twinning

  Andrea Thorn

  Lecture Notes, Handouts and Tutorial material:

  • Andrea's Shelx page

  Refinement

  Garib Murshudov

  Refmac webpage for Presentationas and Tutorials (includes Jligand):

  • Garib's Refmac page

  Lecture notes:

  • Refinement with Refmac5 (pdf)
  • Dictionary of Ligands (pdf)

  ARP/wARP

  Victor Lamzin, Ciaran Carolan

  Lecture Notes:

  • Interpretation of 3D electron density and model building with ARP/wARP (pdf)
  • ARP-Ligand: Locating, identiying and building ligands in electron density (pdf)

  Deposition and Structure Analysis

  Nobutoshi Ito, Eugene Krissinel, Charles Ballard

  Lecture Notes:

  • Protein Data Bank and Deposition to the PDBj (pdf)
  • Macromolecular Complexes in Crystals and Solutions (pdf)
  
  

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