Hi, I'm a little stuck with a Pymol script. I'd like to represent my protein with fancy helices and B-sheets, and in a looped domain I want to show a few residues, but only the side chains.
In my script I tried using "set cartoon_side_chain_helper, on, HISA" on the selection of residues I want to show, but I still get the rest of the side chain displayed. In the script window I can see that it loads this command, but it does not seem to lead to what I want. I'm using Pymol 1.4, so I suppose it is recent enough for this script to work. Below is a section of my script. Help will be gratefully appreciated. Chris B xxxxxxx SCRIPT xxxxxxx load gpV-trimer.pdb, gpVabc center gpVabc #util.ss gpVabc hide everything, gpVabc create VA, (gpVabc//A/6:211/) alter VA//A/45:47/, ss='S' #show ribbon, A #set ribbon_width=8, ecr20e set cartoon_fancy_helices=1, VA show cartoon, VA #set cartoon_transparency=0.7, VA #set cartoon_rect_length=0.75, VA color salmon, VA #hide everything, (VA//A/128:211/) create HISA, (gpVabc//A/197,199/) show sticks, HISA set cartoon_side_chain_helper=1, HISA color gray40, (HISA and elem C) color red, (HISA and elem O) color blue, (HISA and elem N) color yellow, (HISA and elem S) set stick_radius=0.20, HISA #hide everything, HISA -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
