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CCP4 Molecular Graphics (CCP4MG)

CCP4 Molecular Graphics (CCP4MG). What is CCP4MG ？. Software developed by Liz Potterton and Stuart Mc Nicholas in the university of York to create publishing quality images and animation for articles, reports or presentations. http://www.ysbl.york.ac.uk/~ccp4mg/. How to use CCP4MG?.

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CCP4 Molecular Graphics (CCP4MG)

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  1. CCP4 Molecular Graphics(CCP4MG)

  2. What is CCP4MG ？ Software developed by Liz Potterton and Stuart Mc Nicholas in the university of York to create publishing quality images and animation for articles, reports or presentations. http://www.ysbl.york.ac.uk/~ccp4mg/

  3. How to use CCP4MG? • CCP4MG is separated in two windows: • The Display Table • The Graphics Window

  4. Atomic Coordinates (PDB/mmCIF) • Opening the coordinates file:

  5. The Display Table Each molecule or display object can be modify independently from the others. Each molecule file will appear as a 3 columns object Molecule “Object (a model object on this image)”

  6. Atom Selection

  7. Atom Selection

  8. Colour Scheme

  9. Display Style

  10. The Objects

  11. Surface

  12. Close Contacts Temperature Spheroids Annotations Hydrogen Bonds

  13. Electron density maps (MTZ/MAP)

  14. Crystals Display Options

  15. Maps Display Options

  16. Now let’s have some fun !

  17. Superpose Proteins

  18. Movies

  19. Movies

  20. Movies

  21. Let’s have some more fun!!

  22. Let’s have some more fun!!

  23. Other interesting things Applications -> Geometry Tools -> “Global controls” Monomer definition Preferences File -> Output screen Image View -> stereo show axes Transparency (!!) Model object -> add legend

  24. What you see is not alwaysas good as what you get! There are various options in CCP4MG that let you tune the performance of the display in order for interaction to be as fast as possible. This does not affect the results of pictures !!

  25. COOT

  26. What is COOT ？ • Coot is for model building, model completion and validation. • Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots... • Coot is developed by Paul Emsley and Kevin Cowtan from the university of York. http://www.ysbl.york.ac.uk/~emsley/coot

  27. How to use COOT?

  28. The “File” Menu

  29. The “Calculate” Menu

  30. The “Calculate” Menu

  31. The “Calculate” Menu

  32. The display manager

  33. The “Validation” Menu

  34. The “Validation” Menu

  35. Thank you for your attention Any

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