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CCP4 Molecular Graphics (CCP4MG). What is CCP4MG ? Software developed by Liz Potterton and Stuart Mc Nicholas in the university of York to create publishing.

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Presentation on theme: "CCP4 Molecular Graphics (CCP4MG). What is CCP4MG ? Software developed by Liz Potterton and Stuart Mc Nicholas in the university of York to create publishing."— Presentation transcript:

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. 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: a)The Display Table b)The Graphics Window

4 Atomic Coordinates (PDB/mmCIF) 1)Opening the coordinates file:

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

6 Atom Selection

7

8 Colour Scheme

9 Display Style

10 The Objects

11 Surface

12 Hydrogen Bonds Close ContactsTemperature SpheroidsAnnotations

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

20

21 Let’s have some more fun!!

22

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

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 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 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.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

31

32 The display manager

33 The “Validation” Menu

34

35 Thank you for your attention Any


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