>> The system I am studying has an amide of interest (oleamide) in oil (At >> the moment just dodecane molecules). >> I have seen in the manual how to select individual elements, but is it >> possible to select either the Nitrogen or oxygen in my oleamide >> molecules, and then select all atoms which are bonded to this to >> therefore select the entire oleamide molecule.
PyMOL has some powerful selection operators, here are a few that might help you: (1) Select a complete residue based on one atom select aRes, br. someAtom (2) Select a complete molecule based on one atom: select aMol, bm. someAtom (3) Select all atoms bound to another atom: select boundTo, neighbor someAtom (4) Select organic small molecules select myLig, org So, if your case I would try: select oleamide, bm. anyOleoAtom If the ligand is bound to the protein, you'll get the entire object, so try "br." instead to get just the ligand. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
