Electron Density Surfaces

Use the Electron Density Surface dialog (Surfaces-Electron Density) to generate surfaces from electron density data.

UI controls are enabled only when data is available for the selected molecule.

Regenerating a surface previously created simply replaces the previously generated surface.

The rendering style can be changed after the surface has been generated.

Checking the "Real-time Update" checkbox will cause a surface to be re-generated without having to press the Generate button each time any value in the dialog box changes.

The following settings are persistent across sessions (i.e. will be stored on disk and retrieved when Molekel starts):

• Isosurface value
• Use both signs
• Generate Nodal Surface
• Sep Size
• Transparency
• Color

The bounding box size is not saved and each time the dialog box opens the bounding box size is set to the current molecule's bounding box size.

Add density matrix surface

1. Check Density Matrix checkbox
2. Adjust bounding box and step
3. Select rendering style
4. Press the Generate button

Remove Density Matrix surface

1. Check Density Matrix checkbox
2. Press the Remove button

Add orbital surface

1. Click on the row corresponding to the orbital surface to generate (click on any column except the one with orbital numbers).
2. Adjust bounding box and step
3. Select rendering style
4. Press the Generate button

Remove orbital surface

1. Click on the row corresponding to the orbital surface to generate
2. Press the Remove button

Gaussian 03

In order to visualize molecular orbitals from Gaussian 03 output files the * ATOMIC CENTER * ATOMIC ORBITAL * GAUSSIAN FUNCTIONS * table must be present in the file.

To have the basis functions printed in the correct format for Molekel use gfoldprint and pop=full when running Gaussian 03.

Do not include the word basis in the title line of your Gaussian input file.