CCP4 Molecular Graphics (CCP4MG)
Dec 31, 2015
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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