This image was made for the cover of Alwyn's "O Essentials" manual, and the aim was to produce a high-contrast B&W image of electron density that would survive the printing process. As usual, I used The Gimp, but the principles are the same for Adobe Photoshop.
The procedure was as follows : In "O" I centred on the tryptophan, coloured the object white, and created 0.2mm smooth stick and balls, made opaque by hitting F3. The map was also displayed in white. Then I used xv to capture part of the screen, and saved it as a gif file.
In The Gimp, I first used Image-RGB to change the colour mode from indexed to RGB, to allow continuous colour operators to work, and cropped the image more accurately, since it is easier here than at the capture stage. Then I used Image-Colors-Invert to give a dark image on light background, and Image-Colors-Desaturate to give only grey-scale colours. I also used the lasso to select the trp density, inverted the selection, and cut away the rest of the image. Then Image-Colors-Curves was used to increase the contrast of the darker portions, while not affecting the slightly off-white shadow that was left around the trp after the lasso-cut operation. Finally I converted back to indexed colours with Image-Indexed, and wrote a GIF file which was 'fetched' across to the Mac for Alwyn to put into his word document.