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.

TLSD and Parvati Webservices

Webservices for TLSMD and Parvati.

2011 Lecture Notes and Tutorial Material

To be made available during and after the workshop

...Link to the 2010 course material....

• ARP/wARP
• Balbes
• Buccaneer
• Coot
• Crank
• Data Collection
• HKL
• jLigand
• Ligands
• Molrep
• Mosflm
• MrBUMP
• Parrot/DM
• PDB_Redo
• Phenix
• Pisa
• Refmac
• Shelx
• TLS Refinement
• Twinning
• XDS

ARP/wARP

C. Carolan

Lecture Notes:

• ARP/wARP model building (pdf)
• ARP/wARP ligand building (pptx)

Tutorial Material:

• ARP/wARP tutorial(pdf)

Molrep

Andrey Lebdev

Lecture Notes and Tutorial Material:

• Molecular Replacement with Molrep (pdf)

Mosflm

A. Leslie

Lecture Notes:

• Diffraction Data Processing with iMosflm, Pointless and Scala (ppt)

Tutorial Material:

• Mosflm tutorial for the new interface (pdf)

MrBUMP

Ronan Keegan

Lecture Notes:

• MrBUMP - Automated Molecular Replacement (pdf)

Tutorial Material:

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

Shelx

Tim Gruene

Lecture Notes and Tutorial Material:

• Macromolecular Phasing with Shelxc/d/e

Twinning

Z. Dauter & A. Lebedev

Lecture Notes:

• Twinning in protein crystals (ppt)
• Twinning and other pathologies (ppt)
• Space group assignment in the presence of pseudosymmetry and twinning (doc)

Balbes

Garib Murshudov

Lecture Notes:

• Link to Balbes manual

Buccaneer

Raj Pannu

Lecture Notes:

• Buccaneer (ppt)

Tutorial Material:

• Phasing, phase improvement and model building in CCP4 (pdf)

Coot

Bernhard Lohkamp

Lecture Notes:

• Model Building with Coot - An Introduction (pdf)
• Ligand Fitting and Validation with Coot (pdf)

Tutorial Material:

• Link to Coot tutorials page
• Model building with Coot tutorial (pdf)
• Coot Tutorial 2 (ligands and validation) (pdf)

Crank

Navraj S. Pannu

Lecture Notes:

• Structure solution with Crank (pptx)

Tutorial Material:

• Phasing, phase improvement and model building in CCP4 (pdf)

Data Collection

Zbigniew Dauter

Lecture Notes:

• Data collection strategy (ppt)

HKL

Dominika Borek

Lecture Notes:

• HKL2000/HKL3000 (pdf)

jLigand

Andrey Lebedev

Tutorial material:

• jLigand tutorials and download information

Phenix

Tom Terwilliger & Paul Adams

Lecture Notes:

• Automated Structure Determination (ppt)
• Phenix refinement (pdf)
• Validation with Molprobity (pdf)

PISA

Eugene Krissinel

Lecture Notes:

• PISA (pdf)

Tutorial Material:

• PISA Tutorial (pdf)
• PISA Manual (doc)

Refmac

Garib Murshudov

Lecture Notes:

• Refinement of Macromolecular structures using REFMAC5 (pdf)

Tutorial Material:

• Refmac tutorial material

PDB_Redo

Robbie Joosten

Lecture Notes:

• TLS and all that (pdf)

TLS Refinement

Ethan A. Merritt

Lecture Notes:

• TLS and all that (pdf)