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Visualisation with the CCP1GUI

Getting Started

The GUI does not yet have a user manual, but the following sections should provide some help in trying out the code and seeing what is there now. In many cases context-sensitive help is available using the F1 key.

Please read through the bugs and limitations pages help avoid frustration when you try to run something which is not yet implemented, and work through the examples in the order given as information is not repeated.

Structure of a molecule

In the data directory you will find a file ch3oh_potential.pun which you can read in with the File->Open.

For each "object" (this general classification includes both molecules and numerical data fields) in the data file there will be an option on the Views menu.

The first entry on this menu, labelled "Methanol" will be portrayed in a bold font, denoting the fact that an image of this object is being displayed. A submenu will provide the option of removing the image "Hide.." and changing the settings for the image "Adjust..". Using the panel that comes up when you use the Adjust... option you can add sphere, stick, and label representations. After each change, press Update to rebuild the images.

Clicking right-mouse on an atom will cause the atom details (bond lengths and angles) to be printed. The output will appear in the window from which the GUI was started, unless you have opened the Idle Shell (Shell menu). The Idle shell is not yet available if you are using Python 2.3.

Charge Density, Potential and Orbitals

The remaining objects are data fields, the values of scalar data fields at a grid of points (a 51x51x51 3D grid in this case). By default, no default view of data fields is generated, "Orbital View" for the HOMO and LUMO. For the density, you can use the "Density View", to get a simple isosurface. You can create multiple surfaces by repeating the operation and setting different contour heights using the "Adjust ..." option and make the outer ones partially transparent by reducing the Opacity.

To examine the potential, first try colouring an isosurface representation of the charge density. View the Density with the colour surface view, and then adjust this to set the colour field to "potential". You adjust the parameters to change the view, for example change the way potential is mapped to colour using the colourmapping entry boxes which indicate which potential values correspond to the low and high ends of the rainbow colourmap.

Then try the Cut Slice View on the potential sub-menu. A control panel will appear, increae the value of the X Scale and Y Scale slides to the cut slice grid to take a large slice, and move it through the space around the molecule using the translate and rotate options.

Vibrational Modes of Ethane

Open the file examples/ethane_vib.pun. The Views menu will now contain an entry for each vibration labelled by the frequence in wavenumbers, -ve values denoting the imaginary frequencies. In each case the relevant submenu will have a single entry, which will create an animation of that mode. You may want to hide the view of the molecule before starting the animation using the button on the control panel.

Viewing a Periodic Structure

The file examples/sodalite.c provides a suitable example to try out the Extend option on the Edit menu, which will allow a number of unit cells to be visualised using the molecule visualiser.

Return to the CCP1GUI homepage

For more information about the work of the Computational Chemistry Group please contact Paul Sherwood p.sherwood@dl.ac.uk or Bill Smith w.smith@dl.ac.uk
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