Hi Stephane, You don't have phi/psi angles, so determining secondary structure is a bit problematic. What you can do is draw a trace through the backbone beads and set the secondary structure representation explicitly. You'll have to make sure to exclude connections between chains.
set cartoon_trace_atoms show cartoon, CG_protein and n. bb cartoon helix cartoon loop, i. 1-10 # and so on... Hope it helps, Tsjerk On Mon, Mar 4, 2013 at 4:03 PM, ABEL Stephane 175950 <stephane.a...@cea.fr> wrote: > Hello everybody, > > I have done several MD simulations with the Martini force field of systems > that contain a small protein and surfactant with GROMACS. It is possible to > show with pymol the secondary structure of the protein with a cartoon > representation and the detergent molecules with beads at the same time. I > know from you that I can use for the detergent molecules, the "connects" but > for protein i don't know how to do (with the alter command?). > > Can you help me? > > Thanks you in advance > > Stephane > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
