Difference between revisions of "Tutorials"

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The tutorials can be used for class teaching.
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;Example Scripts
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:Copy and edit to start using Phaser
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:* [[Keyword Example Scripts | Keyword Example Scripts]]
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:* [[Python Example Scripts | Python Example Scripts ]]
  
* [[MR using CCP4i:TOXD|MR using CCP4i:TOXD]]
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;Tutorials
* [[MR using CCP4i:BETA/BLIP|MR using CCP4i:BETA/BLIP]]
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:The tutorials are suitable for individual use or class teaching.
* [[MR using keyword input|MR using keyword input]]
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:* [[MR using CCP4i:TOXD|MR using CCP4i:TOXD]]
* [[Finding a search model:TOXD|Finding a search model:TOXD]]
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:* [[MR using CCP4i:BETA/BLIP|MR using CCP4i:BETA/BLIP]]
* [[SAD using CCP4i|SAD using CCP4i]]
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:* [[MR using keyword input|MR using keyword input]]
* [[Combined MR-SAD using CCP4i|Combined MR-SAD using CCP4i]]
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:* [[Finding a search model:TOXD|Finding a search model:TOXD]]
:[[Image:Download.png]] [[Data for Tutorials]]
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:* [[Molecular replacement with MRage]]
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:* [[SAD using CCP4i|SAD using CCP4i]]
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:* [[Combined MR-SAD using CCP4i|Combined MR-SAD using CCP4i]]
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:* [[EP using Phenix|EP using Phenix]]
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:* [[SCEDS using CCP4i|SCEDS using CCP4i]]
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:* [[SCEDS for MR (using keyword input)|SCEDS for MR]]
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:* [[NMA Coordinate Perturbation using CCP4i|NMA Coordinate Perturbation using CCP4i]]
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;Coot script for Normal Mode Analysis - Perturbations (NMAXYZ)
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: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.
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  def all_molecules_to_CA():
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    for imol in model_molecule_list():
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        graphics_to_ca_representation(imol)
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  coot_toolbar_button("CA", "all_molecules_to_CA()", icon_name="6-c.svg")
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  coot_toolbar_button("pre-CA", "set_default_representation_type(4)",icon_name="5-c.svg")
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;Data
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:The coordinate (pdb), sequence (fasta) and reflection (mtz) files required to run the MR tutorials are distributed with Phaser.
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:[[Image:Download.png|link=]] [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/phaser-mr-tutorial.tar.gz  Data for Molecular Replacement Examples and Tutorials]
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:[[Image:Download.png|link=]] [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/phaser-ep-tutorial.tar.gz  Data for Experimental Phasing Examples and Tutorials]
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:[[Image:Download.png|link=]] [http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/phaser-sceds-tutorial.tar.gz  Data for SCEDS Examples and Tutorials]
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;References
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: 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.
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: The crystal structure of insulin phased on intrinsic sulphurs. We thank Paul Adams for the diffraction data. Reference: Adams (2001) ''Acta Cryst'' D'''57'''. 990-995.

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.