James, > Is there any semi-avtomated way to find ligand binding pocket and do all > such things ?
For your given object, click A > preset > ligands sites > cartoon. Try other options under that menu. Cheers, -- Jason > 2011/11/28 Thomas Holder <spel...@users.sourceforge.net> >> >> Hi James, >> >> most trivial manner: >> >> as cartoon >> show sticks, resn LEU+ILE+VAL >> set cartoon_side_chain_helper >> >> and eventually something like this: >> >> show spheres, resn LEU+ILE+VAL and not name N+O+C >> set sphere_transparency, 0.5 >> >> >> Cheers, >> Thomas >> >> On 11/28/2011 02:58 PM, James Starlight wrote: >>> >>> Another question also linked with the non-covalent interaction. >>> >>> In particular I wounder to know how i Could represent all hydrophobic ( >>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd >>> like to represent the hydrophobic core of the proteins made from those >>> residues. >>> >>> Thanks, >>> >>> James >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen > > > ------------------------------------------------------------------------------ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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
