Try changing the transparency setting to Multi-Layer -- this will prevent the 2nd overlapping surface from appearing "solid" (assuming I understand you correctly)
In the PyMOL menu bar, go to: Setting > Surface > Multi-Layer Hope that helps! Kip On Oct 2, 2012, at 11:09 AM, Christopher Browning wrote: > Dear All, > > I was wondering if anybody knows how one can have two transparent > surfaces overlapping but then being able to see how the 2 intersect > using PYMOL. At the moment, if I have two transparent surfaces > overlapping I don't see how they overlap internally, only externally. I > can see how they overlap internally if one surface is transparent and > the other is solid, but that is not quite what I'm after. > > Hope you can help. > > Chris > > > -- > Dr. Christopher Browning > Post-Doctor to Prof. Petr Leiman > EPFL > BSP-416 > 1015 Lausanne > Switzerland > Tel: 0041 (0) 02 16 93 04 40
