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.

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. MAIN provides very good graphics for this type of image. The depth cueing is done at the command level and can be reproducibly controlled. Density may be removed atom by atom allowing, for example, only the density for a side chain to be displayed. The script for this image is available. The image is saved using snapshot.

Last Modified: Thursday, 02-Jul-1998 14:46:33 EDT
Comments to Pat Fleming (fleming@csb.yale.edu) appreciated.