Tutorials

Example Scripts

Copy and edit to start using Phaser

• Keyword Example Scripts
• Python Example Scripts

Tutorials

The tutorials are suitable for individual use or class teaching.

• MR using CCP4i:TOXD
• MR using CCP4i:BETA/BLIP
• MR using keyword input
• Finding a search model:TOXD
• Molecular replacement with MRage
• SAD using CCP4i
• Combined MR-SAD using CCP4i
• EP using Phenix
• SCEDS using CCP4i
• SCEDS for MR
• NMA Coordinate Perturbation using CCP4i

Phubuntu

Phubuntu is an Ubuntu Linux boot iso file is available from Phenix

This method of installation is very useful for running tutorials/workshops with participants using their own laptops as it circumvents the problems associated participants having heterogeneous operating systems and different Phenix versions installed

Burn this file to a DVD and use it to boot your computer and run Phenix and Coot

More information on Phubuntu

Coot script for Normal Mode Analysis - Perturbations (NMAXYZ)

To add a button to Coot to convert all loaded molecules to CA representation (C-alphas/backbone in the Display Manager) put the following script (called e.g. all-to-ca.py) in your .coot-preferences directory. Jiffy courtesy of Paul Emsley.

 def all_molecules_to_CA():
   for imol in model_molecule_list():
       graphics_to_ca_representation(imol)
 coot_toolbar_button("CA", "all_molecules_to_CA()", icon_name="6-c.svg")
 coot_toolbar_button("pre-CA", "set_default_representation_type(4)",icon_name="5-c.svg")

Data

The coordinate (pdb), sequence (fasta) and reflection (mtz) files required to run the MR tutorials are distributed with Phaser.

Data for Molecular Replacement Examples and Tutorials

Data for Experimental Phasing Examples and Tutorials

Data for SCEDS Examples and Tutorials

References

The crystal structure of a hetero-dimer of beta-lactamase (BETA) and beta-lactamase inhibitor protein (BLIP), both with molecular replacement models from crystal structures of the individual BETA and BLIP components. We thank Mike James and Natalie Strynadka for the diffraction data. Reference: Strynadka, N.C.J., Jensen, S.E., Alzari, P.M. & James. M.N.G. (1996) Nat. Struct. Biol. 3 290-297.

The crystal structure of insulin phased on intrinsic sulphurs. We thank Paul Adams for the diffraction data. Reference: Adams (2001) Acta Cryst D57. 990-995.