Below is a comparison of electron density with stick figures made by several graphics programs here in the CSB core lab. Only one residue in the protein is contoured with electron density to include masking in the example. The example scripts will give you an idea of how to make your own similar figure.

Look at the individual documentation linked to the previous page for information on starting these applications.

Click on the image for a larger view.

	SPOCK will display electron density maps. SPOCK also will do antialiasing for crisp images. The commands to create an image similar to this one are available here. The image is saved as *.rgb for this image but other options are available.
	RIBBONS will display electron density maps. RIBBONS also has a GUI to create the files necessary for such a display and it also will do antialiasing for crisp images. The commands to create an image similar to this one are available here. The image is saved as *.rgb using a system call.
	A combination of O, plt2mol.pl and Molscript was used to generate this Postscript image. It requires some file editing but the Postscript output provides crisp electron density lines. The The script for this image is available.
	O will generate this type of image. The depth cueing must be done by using the slab and z-translation dials. Density contour masking may be done for whole residues including the backbone atoms only. The script for this image is available. The image is saved using snapshot.
	O can be used to generate stereo images also. The script for this image is available.