Having put the "make my density look publishable" (mapcover) command in BobScript, my conscience wouldn't ever let me use it as it gives a false impression of experimental maps!
It is useful, though, in a couple of cases: where the map is not representing electron density but calculated from the structure (e.g. binding pockets...) and - artistic tip for the day - to draw a map in two colours which I have used in presentations to help show ligand density. You draw the map in one colour, then increase the map line width ever so slightly and draw it again with map cover and in a different colour. The ligand density is then highlighted but the rest of the structure and noise are still visible. However, the original question seemed to be targeted at obscuring information (the ligand structure) rather than showing it. I assume this is not for academic purposes! My suggestion there would be to use a low resolution map (say calculated to 3.5A) covering where the ligand is and the full resolution map for the rest of the molecule. (Effectively rendering the ligand density as a blob). Otherwise Tassos is spot on... use Illustrator... Cheers, Robert
