Hi James, The menu action uses the "dss" command, so the result should be exactly the same.
Remove loops: PyMOL> remove not ss H+S There are several h_bond settings which tune the dss command: PyMOL>grepset h_bond h_bond_cone : 180.00000 h_bond_cutoff_center : 3.60000 h_bond_cutoff_edge : 3.20000 h_bond_exclusion : 3 h_bond_from_proton : on h_bond_max_angle : 63.00000 h_bond_power_a : 1.60000 h_bond_power_b : 5.00000 Alternative to "dss" is to use external applications like "dssp" or "stride". You can run them within PyMOL if you install a plugin: http://pymolwiki.org/index.php/Dssp_stride Cheers, Thomas James Starlight wrote, On 03/08/12 09:43: > Dear PyMol users! > > I'm working with the big pdb ensemble wich lack information about the > secondary structure ( deleated header region) > > I want to find possible way to assign secondary structure for all pdb's > in my ensemble ( like A-> assign sec.str for specified pdb). Finally I > want to deleate some common SS region is the whole insemble -e.g all > loops etc. > > I've already found command wich can do that i want- dss but assignment > done by that command is less correct than the above method ( via contex > meny) wich i use for specified structure. > > Is there any alternatives? > > Thanks for help, > > James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ 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
