Hi James, ramachandran plot for the *current* state can be created with the DynoPlot plugin: http://pymolwiki.org/index.php/DynoPlot
It uses the API function "get_phipsi", which can calculate phi/psi angles for given states: cmd.get_phipsi(selection='(name ca)', state=-1) Torsion angles other than phi/psi can be calculated with the "get_dihedral" fuction: http://pymolwiki.org/index.php/Get_Dihedral You can also modify torsion angles with "torsion" and "set_dihedral": http://pymolwiki.org/index.php/Set_Dihedral http://pymolwiki.org/index.php/Torsion And you can modify torsion angles interactively using the mouse while in editing mode (pick one atom, then CTRL-Drag). Hope that helps. Cheers, Thomas On 11/16/2011 06:50 PM, James Starlight wrote: > Dear PyMol Users! > > I wounder to know about posible ways to plot for my structures different > torsion angles (phy, psi, chi ) on the ramachandran map via pymol. > > In particular I would like to obtain the next information > > 1- I d like to visualise and measure different torsions for my structure > and plot this values on the ramachandran plot > > 2- I'd like to make such measurements for the enssemble of the pdb > structures and plot on the ramachandran map values for each structure ( > by points or other markers) > > Finaly could you show me some tutorials wich could help me working with > torsions in pymol? > > Thanks for your help, > > James -- Thomas Holder MPI for Developmental Biology ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
