http://baoilleach.blogspot.com/2010/06/visualising-orbitals-and-density-with.html

http://baoilleach.blogspot.com/2010/06/visualising-orbitals-and-density-with.html

Note: there is an excellent article on how to visualize electron density data from Gaussian 09 files here: http://baoilleach.blogspot.com/2010/06/visualising-orbitals-and-density-with.html

Another video available here: http://molekel.cscs.ch/video/orbitals_big.htm shows how to generate orbitals.

Videos

Another video available here: http://molekel.cscs.ch/video/orbitals_big.htm shows how to generate orbitals

A video showing how to generate electron density surface with color coded Electrostatic Potential values is here: http://molekel.cscs.ch/video/eldens_big.htm ... ...and another one showing the use of real-time update to adjust the bounding box is here: http://molekel.cscs.ch/video/eldens_rt_update_big.htm

Hint - Use low-resolution (i.e. large step size) and check the real-time update box while adjusting the bounding box: the surface will be quickly recomputed at each change of the bounding box parameters; you can then decrease the step size as needed.

A video showing how to generate electron density surface with color coded Electrostatic Potential values is here: http://molekel.cscs.ch/video/eldens_big.htm

note: If you just want to visualize IR spectra (Freq=HPmodes) you don't need gfoldprint

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

If you just want to visualize IR spectra (Freq=HPmodes) you don't need gfoldprint

The rendering style can be changed after the surface is generated.

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

http://molekel.cscs.ch/wiki/uploaded/ReferenceGuide/ui_el_dens_bbox_small.png

Use the bounding box size and center to select the volume of interest.

http://molekel.cscs.ch/wiki/uploaded/ReferenceGuide/ui_el_dens_bbox.png

Hint - Use low-resolution (i.e. large step size) and check the real-time update box while adjusting the bounding box: the surface will be quickly recomputed at each change of the bounding box parameters; you can then decrease the step size as needed.

http://molekel.cscs.ch/wiki/uploaded/ReferenceGuide/ui_el_dens_dlg.png

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

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

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

(:title Electron Density:)

http://molekel.cscs.ch/wiki/uploaded/ReferenceGuide/eldens_dlg.png

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

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

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.

1. Click on the row corresponding to the orbital surface to generate (click on any column except the one with orbital numbers).

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.

Checking the "Real-time Update" checkbox will cause all the changes to any value in the dialog to be applied immediately without having to press the Generate button.

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

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

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

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

http://bioinformatics.org/molekel/uploads/ReferenceGuide/eldens_dlg.png

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
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

Update in progress

Electron Density Surfaces

Orbitals and surface from density matrix can be generated by opening the Electron Density Surface dialog (Surfaces-Electron Density).

http://bioinformatics.org/molekel/uploads/ReferenceGuide/eldens_dlg.png