Julio Cesar da Silva wrote: > I have a doubt about how to superpose two molecules in a molecular viewer. > I need to superpose two protein structure in a spacefill representation. I > would like to show one of them with semi-transparency. I have tried to do > this in the softwares Rasmol and Pymol, but I could not. I would like to > show both of them at same time and can see both. So, I would like to show > one semi-transparent and the other one normal. Please, does someone know > how to do this? Could you help me? Thanks. You could download the freeware 'YASARA View' from http://www.yasara.org Here is what the result would look like: http://yasara3.cmbi.ru.nl/service/transsup.jpg The steps are: - Show the first molecule in spacefill representation - Create a transparent VdW surface for the second molecule - Hide the atoms of the second molecule - Raytrace the result, choosing a 'ball zoom factor' of 1.5 (this makes sure the size of the spacefill representation matches the VdW radii). Good luck, Elmar -- Elmar Krieger, PhD YASARA Biosciences & CMBI Outstation Austria Neue-Welt-Hoehe 13/b A-8042 Graz Austria/Europe Ww c(@@)c ================()==OUu============ =WHAT IF YASARA knows the answer?!= =----- http://www.yasara.org -----= =- http://www.cmbi.kun.nl/whatif -= ============OOo==================== () () _/ /_