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.

YSBL Webservices - Balbes, etc..

Webservices from the YSBL, York University, UK. Services include BALBES, Buccaneer, SfCheck and others. YSBL Webservices.

2011 Lecture Notes and Tutorial Material

To be made available during and after the workshop

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)

Supported by: