Collaborative Computational Project No. 4 Software for Macromolecular X-Ray Crystallography

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.

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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