Hi Christopher, I saw your script and there's many ways to the same destination. Here's how my brain thinks:
load A.pdb hide everything, A show cartoon, A [cmds for whatever else I like: fancy helices etc. etc.] Option 1: show sticks, A and resi 197-199 Option 2: And if you hate that the backbone CA sticks out in an ugly manner say for resi 197 on the cartoon, then do: hide sticks, A and resi 197 and resn CA (...or even just...) hide sticks, A and and resn CA (made hide CA you don't want...) Hope this helps. Raji On Fri, Jul 15, 2011 at 9:52 AM, Christopher Browning < [email protected]> wrote: > 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 > -- ---------------------- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
