By using pymol, i am going to represent the surface of protein. It's is done when i click on the Show>surface. But i want to highlighted some residue above the surface of the protein (Like in attached fig). How i can do this?
Just select the residue you'd like to highlight (either on the graphic interface - clicking on it or displaying the protein sequence on top of the main window- or by using the command line - select "surf-res", i. "insert residue number"-). Once you have the residue selected, just use the menu on the graphic interface to display it as stick.
thanks for ur comments on question. i think you dont understand what i am asking.. first i will represent the surface. Then with surface model i want that i have highlight some residues that will appear above the surface as shown in attached fig. The problem is that when i showed the surface and want to represent the residue above the surface, the residues are in the mid of the protein so they cant highlighted due to the upper surface model.
After you have selected the residue and displayed it as a stick, you will have to hide the surface representation for that selected residue in order to show it over the surface of the protein.
What I don't understand is what you mean by the residue being in the mid of the protein: is that residue a surface one or is it buried? If the residue is not on the surface of the protein, but "on the inside", I am afraid you won't get anything similar to the example figure you've attached. In that case, you may want to play around with the transparency of the surface representation. By making the surface 40-50% transparent (maybe more, that will depend on your preference), you will be able to show a residue displayed as a solid stick in the inside of the protein.
Maybe you could attach a picture of your structure, pointing out where the residue is? That way I'd get a better a idea of the specific problem.
Do you want to have a surface model and stick model? Can you represent your protein as surface, set transparency of surface to 50%, and then select the residues you want represent as stick and diplay/label.
Another (could be weird way but can surve your purpose) is to select your whole protein (except the residues of interest). Create the selection as an object1 and display it as surface. Then choose your residue of interest, create them as object2, and display them as sticks.
I created one for ubiquitin, while highlighting K27 according to your desired representation.