Hi Annalisa, The Chimera Multiscale tool makes a low resolution surface for each chain of a PDB model. You could put all of type A surfactant molecules in one chain, and all type B surfactant molecules in another chain. Open the model in Chimera (menu File / Open) then use menu entry Tools / Higher-Order Structure / Multiscale Models, select Multimer type "None" at the bottom of the dialog and press the "Make models" button near the bottom. You'll probably want a higher surface resolution than the default 8 angstroms. Press the Select "All" button at the top of the multiscale dialog, then change the resolution value (middle of dialog) from 8 to 3 and press the Resurface button. By using two PDB chains you will have two surfaces -- one for each type of surfactant. Each can be colored by selecting it (hold ctrl and click on it with mouse button 1), then press the Color button in the multiscale dialog and choose a new color. The multiscale dialog is also able to use matrices to position copies of molecules as Elaine noted. But since your surfactant molecules are all in different conformations I don't think that will help you. Tom