CCP4 Molecular Graphics Documentation
	Contents

Documentation Contents

General

• Graphics window - mouse bindings and short cuts
• The display table - control the data and display objects
• The View menu
• The Display menu
• Projects - data organisation
• Installation of support programs
• Compiling CCP4MG

Molecular models

• Reading coordinate files and atom typing
• The Coordinate Model Interface
• Atom selection
• Structure Analysis
• Surfaces and Electrostatic Potentials
• Symmetry Related Models
• Animations
• PISA Analysis of Model Interfaces

Other types of data

• Electron density maps
• Vectors
• Text and imported images

Applications

• Superpose automatic protein superposition and interactive superposition of any structures
• Presentation Graphics
• Picture Wizard set up complex pictures quickly
• Movies
• Presentations
• Geometry
• Run Coot

Other utilities

• Lighting
• Saving the program status
• Picture Definition Files (also Object attributes and Introduction to Python)
• Making presentations

See Display Table for general overview of the display table.

Windows Bring a 'lost' window to the front.

• http://www.ccp4.ac.uk/MG//ccp4mg_help/index.html has the latest help pages which may have more information.

• Presenting your structures: the CCP4mg molecular-graphics software
  S. McNicholas, E. Potterton, K. S. Wilson and M. E. M. Noble
  Acta Cryst. (2011). D67, 386-394
• Developments in the CCP4 molecular-graphics project
  L. Potterton, S. McNicholas, E. Krissinel, J. Gruber, K. Cowtan, P. Emsley, G. N. Murshudov, S. Cohen, A. Perrakis and M. Noble
  Acta Cryst. (2004). D60, 2288-2294
• The CCP4 molecular-graphics project
  E. Potterton, S. McNicholas, E. Krissinel, K. Cowtan and M. Noble
  Acta Cryst. (2002). D58, 1955-1957
• If you use the remote blast service at the EBI you should refer to:
  Web services at the European Bioinformatics Institute-2009
  Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp302
  A new bioinformatics analysis tools framework at EMBL-EBI
  Nucl. Acids Res. (2010) 38 (suppl 2): W695-W699. doi: 10.1093/nar/gkq313
  
• If you use PISA you should refer to:
  Inference of macromolecular assemblies from crystalline state.
  E. Krissinel and K. Henrick (2007).
  J. Mol. Biol. 372, 774-797.