On May 18, 2007, at 12:29 AM, 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. > hi Júlio, I'm sure many programs can do what you want. here is how to do it in Jmol: launch Jmol.app and bring up a scripting window. then issue the following commands (for example): # use the 'load files' command to load multiple files load files "file1.pdb" "file2.pdb" # file1.pdb can be accessed as model 1.1 # use the 'color translucent' command to control translucency of atom spheres select model=1.1 wireframe off spacefill 100% color cpk color translucent 0.5 # file2.pdb can be accessed as model 2.1 select model=2.1 wireframe off spacefill 100% color cpk # note: the 'select' command does NOT change what is displayed! # use the 'model' command to toggle display. # show only model 1.1 model 1.1 # show only model 2.1 model 2.1 show all models model 0 Jmol has a number of animation controls as well; check out the interactive documentation (esp. the 'frame' command) for all the details: <http://www.stolaf.edu/academics/chemapps/jmol/docs/> hope that helps, tim -- Timothy Driscoll em: molvis at vbi.vt.edu Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07. We will not forget you.