|Molecular Graphics - Functionality|
The following description refers to version 2.5.
The range of model drawing styles include ribbons, surfaces, spheres and ball-and-stick. Surfaces can be coloured by electrostatic potential calculated by the built-in Poisson-Boltzmann method. Nucleic acids can be drawn with ribbons, base blocks or base pair sticks. CCP4mg also displays electron density as cylinders or 2D slices, text with fine control over colour and font and any vectors in a range of styles. You can set up complex pictures quickly using the Picture Wizard and fine tune images with the display table and customised drawing styles.
The Movie interface is entirely GUI-controlled (no scripting) and besides changing the view and position of objects through a movie scene you can change properties such as the electron density contouring level. Animations can be replayed and recorded in movies.
The Superpose application has the SSM automated protein superpostion. The program will calculate and display properties such as secondary structure, hydrogen bonds, solvent accessible surface and surface contact area.
There is a sequence viewer/alignment tool and an approximate normal modes viewer. The command line verison of PISA for exploring macromolecular interfaces and assemblies is included with the program.
There is extensive on-line documentation and quick-start tutorials.
The Picture Wizard is an illustrated library of templates from which you can choose a picture style to apply to your structure. There is also a menu for selecting a picture style as you select a coordinate file.
The picture can be customised and extended using the Display Table which lists all the displayed objects and provides access to extensive atom selection and colouring options.
The drawing styles such as ribbons can be customised.
Surfaces can be coloured by electrostatic potential which is calculated by a built-in Poisson-Boltzmann method. They can also be coloured by any of the colouring criteria applied to the atoms beneath the surface. Surfaces can be displayed as solid, dots or mesh; their extent can be limited to a selection of atoms and they can be transparent.
Molecular models can be drawn in many styles including: ribbons, tubes-and-worms, spheres and ball-and-stick. Nucleic acids can be drawn as ribbons, base blocks and base sticks; lipids and membrane can be drawn in carton style. Properties such as secondary structure, hydrogen bonds, thermal ellipses, solvent accessibility and contact area can be calculated and displayed.
Electron density maps can be loaded from CCP4 map files are calculated from MTZ files. They are displayed as 'continuous crystal' (as in Coot) and can be drawn as mesh, dots, solid or with the mesh lines drawn as cylinders. Maps can be clipped to a selection of atoms.
Text can be added as either Legend on the 2D-screen or Annotation which is attached to a model. The program supports a wide range of fonts and text colouring. Vectors are often useful to point to features, represent atomic interactions or some other property such as the TLS axes. Vectors can be loaded from file or created within CCP4mg and displayed in a variety of styles. Images such as logos can also be displayed and scaled.
CCP4mg makes Images in the usual GIF,JPG,PNG formats. The display is automatically redrawn at optimal quality with options to set image resolution, background transparency and stereo.
You only need to set up the display for the key frames of the movie and save these as 'snapshots' in the Movie interface; the movie will be made by interpolating between the snapshots, smoothly changing properties such as the view, object positions and electron density level. You can preview the movie before recording and refine it by re-saving the snapshots and changing the recording options. The movie is saved as a series of screenshots that are converted to a movie format by helper programs. CCP4mg will automatically run Convert (from ImageMagick), ffmpeg or mencoder to create GIF or MPEG format movies.
The Superpose application uses the Secondary Structure Matching (SSM) method to automatically superpose protein structures. There are also manual tools for selecting atoms, residues (or nucleic acid bases) and ranges of residues or bases to superpose by least squares.
The Geometry application will show inter-atomic distances and angles.
The Presentation application can be used to save a series of scenes and snaphots that can be displayed in the Presentation interface or as part of an HTML file in the built-in browser. Clicking on a snapshot will restore the scene in CCP4mg.
Stereo, clip planes, depth queue fogging, choice of lighting styles and choice of background colour are all supported.
CCP4mg can be run from a command line script with no visible windows using the '-quit' flag. This is most useful for batch mode rendering.