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.

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. Temperature Spheroids
Annotations
Temperature Spheroids
Close Contacts
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
File -> Output screen Image
Tools -> “Global controls”
Monomer definition
Preferences
Applications -> Geometry
Model object -> add legend
View -> stereo
show axes
Transparency (!!)

24. What you see is not always as 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.

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