Difference between revisions of "Tutorials"

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(Delete reference to Phubuntu, which is no longer relevant.)
 
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:* [[SCEDS for MR (using keyword input)|SCEDS for MR]]
 
:* [[SCEDS for MR (using keyword input)|SCEDS for MR]]
 
:* [[NMA Coordinate Perturbation using CCP4i|NMA Coordinate Perturbation using CCP4i]]
 
:* [[NMA Coordinate Perturbation using CCP4i|NMA Coordinate Perturbation using CCP4i]]
 
;Phubuntu
 
:Phubuntu is an Ubuntu Linux boot iso file is available from [http://www.phenix-online.org/download/ 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
 
:[[Phenix-Ubuntu | More information on Phubuntu]]
 
  
 
;Coot script for Normal Mode Analysis - Perturbations (NMAXYZ)
 
;Coot script for Normal Mode Analysis - Perturbations (NMAXYZ)

Latest revision as of 11:16, 6 April 2016

Example Scripts
Copy and edit to start using Phaser
Tutorials
The tutorials are suitable for individual use or class teaching.
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.
Download.png Data for Molecular Replacement Examples and Tutorials
Download.png Data for Experimental Phasing Examples and Tutorials
Download.png 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.