Hi Almu - It's actually even easier than what Vincent wrote as well. :) You don't need to create multiple objects or worry about backbone selections--PyMOL has some built-in settings that will do this for you.
# the PDB from your example fetch 3bwp # color however you like color blue, resi 1-100 color red, not resi 1-100 # show it as cartoon and use PyMOL's ring mode setting to show the bases as cartoon set cartoon_ring_mode, 3 # add transparency, adjust the thickness of the stick representation set cartoon_ring_transparency, 0.5 set cartoon_ring_width, 0.2 # color the rings the same as the rest set cartoon_ring_color, blue, resi 1-100 set cartoon_ring_color, red, not resi 1-100 Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Feb 25, 2015, at 6:58 AM, vincent Chaptal <[email protected]<mailto:[email protected]>> wrote: Dear Almu, very easily: #load the same pdb twice and give it two different names: load xx.pdb, molA load xx.pdb, molB # show one as cartoon, the other as sticks: hide everything show cartoon, molA show sticks, molB #hide the backbone sticks of molB hide sticks, molB and name c+n+o (this is for proteins, for DNA you have to look what are the names to hide). best vincent Le 25/02/15 11:48, Almudena Ponce Salvatierra a écrit : Hi, does anybody know how to represent in pymol a combination of cartoon, with sticks, but without the sticks from the phosphate backbone? I am referring to something like it is in this figure (see attachment). I can get the sticks and the cartoon together for the nucleobases but I don't know how to remove the sticks from the backbone. All suggestions are welcome. Best, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 07 http://www.ibcp.fr<http://www.ibcp.fr/>
