Can conic and ribbonjr images be combined?
Conic and ribbonjr use very different methods for computing images and there is no easy way to combine them. However ribbonjr can be “duped” into displaying space-filling atoms (though without shadows) if that is what is desired. The simplest way to do this is to invoke ribbonjr with the command line flag “-A 1”. This causes all “balls” to be displayed at their full VDW radii (the sticks will still be displayed also, but will be buried inside the balls and therefore not visible). However, if you require both space-filling atoms and balls and sticks in the same image, a more elaborate procedure is necessary. Also, a requirement of the procedure is that the residues that are to be space-filled have names unique from the residues to be depicted normally. This is frequently the case anyway since one of the more common uses of the mixed space-filling/ball-and-stick representation is to show a space-filled ligand with a ball-and-sticked/ribboned receptor. The trick is to make ribbonjr beli
