CCP4 Molecular Graphics Documentation
	QM Fields

Display of Quantum Mechanical Fields

If you are unfamiliar with CCP4mg see the tutorial for quick introduction to displaying atom coordinate files.

QM field (or other data) can be read in from the File menu option Read map and MTZ, sub-option CUBE map file. There is an example of a CUBE file in the tutorial data directory, H2O_OCC.CUBE and the corresponding atom coordinate file is h2o.pdb. By default, on loading the file, one display object, showing a single contour line for one orbital, is displayed. The display table after loading the coordinate file and the field map looks like this:

The three columns in the contour display object line control:

• Selection of orbital
• Colour of orbital for a single contour
• Slider control of contour level

Clicking on the icon will open a menu with additional options:

• Contour mode By default a single contour, at the level controlled by the slider, is displayed. The alternative is to display plus/minus contours which will be coloured red and blue for plus and minus the contour level.
• Set plot plane Chose three atoms to define a plane and then set Surface style to Contour slice to show a slice through the plane of the chosen atoms.
• Surface style By default, the contour surface is shown as 'chicken-wire' lines but this can be changed to Cylinders which give a better appearance when making pictures or set to Transparent for a transparent surface.
• Set opacity Set the opacity of the transparent surface.