CCP4 Molecular Graphics(CCP4MG)

What is CCP4MG ？

Software developed by Liz Potterton Software developed by Liz Potterton and Stuart Mc Nicholas in the and Stuart Mc Nicholas in the university of York to create publishing university of York to create publishing quality images and animation for quality images and animation for articles, reports or presentations.articles, reports or presentations.

http://www.ysbl.york.ac.uk/~ccp4mg/

How to use CCP4MG?CCP4MG is separated in two windows:

a)a) The Display TableThe Display Table

b)b) The Graphics WindowThe Graphics Window

Atomic Coordinates (PDB/mmCIF)

1) Opening the coordinates file:

The Display Table

Each molecule file will appear as a 3 columns object

MoleculeMolecule

““Object (a model object on this image)”Object (a model object on this image)”

Each molecule or display object can be modify independently from the others.

Atom Selection

Atom Selection

Colour Scheme

Display Style

The Objects

Surface

Hydrogen BondsClose ContactsTemperature SpheroidsAnnotations

Electron density maps (MTZ/MAP)

Crystals Display Options

Maps Display Options

Now let’s have some fun !

Superpose Proteins

Movies

Movies

Movies

Let’s have some more fun!!

Let’s have some more fun!!

Other interesting thingsApplications -> GeometryTools -> “Global controls”

Monomer definition

Preferences

File -> Output screen ImageView -> stereoshow axesTransparency (!!)

Model object -> add legend

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 !!

COOT

What is COOT ？

• Coot is for model building, model Coot is for model building, model completion and validation. completion and validation.

• Coot displays maps and models and allows Coot displays maps and models and allows model manipulations such as idealization, model manipulations such as idealization, real space refinement, manual real space refinement, manual rotation/translation, rigid-body fitting, ligand rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, search, solvation, mutations, rotamers, Ramachandran plots...Ramachandran plots...

• Coot is developed by Paul Emsley and Coot is developed by Paul Emsley and Kevin Cowtan from the university of York.Kevin Cowtan from the university of York.

http://www.ysbl.york.ac.uk/~emsley/coot

How to use COOT?

The “File” Menu

The “Calculate” Menu

The “Calculate” Menu

The “Calculate” Menu

The display manager

The “Validation” Menu

The “Validation” Menu

Thank you for your attention

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