I'v been struggling a bit with getting certain (say ligand or cofactors) to pop out of the molecules, in the way as you would choose layers in photoshop. How can I select certain objects or amino acids to be infront of all other layers. e.g. I have a surface representation of a molecules with a cofactor inside, but then I just want the cofactor to pop-out and overlay on top of the surface.
Im a basic (beginner) user of pymol, meaning that im just starting to use commands but i'm not scripting anything for pyMOL yet.
What sort of commands could I use for this?
If want to have an overlay on top of a surface, the only way I see you doing this, is to render (ray) the image twice, once with the surface representation of your protein shown, and once the cofactor alone. Then overlay both pngs (rendered with transparent background, of course) in an image editor of your choice.
If you need both representations inside PyMOL's 3D view, increase the transparency for your surface, and then make sure that only the cofactor is visible as, e.g., licorice representation.