Hi Krisztina, > I wonder if there is any way to list atoms an atom is bonded to?
Use the "neighbor" selection operator: PyMOL> select newsele, neighbor (othersele) See also: http://pymolwiki.org/index.php/Selection_Algebra > I would > like to list H bonded pairs but the available scritps (list_hbonds.py, > or polarpairs.py) only check for distance and angle between heteroatoms, > but not if any of them is actually connected to a hydrogen. As a result > two carbonyl atoms are listed too. Have you also tried the "distance" command? It is very similar to list_hbonds/polarpairs: PyMOL> distance hbonds, all, all, mode=2 There is no direct way to list these pairs, but you can use get_raw_distances script from the PyMOLWiki: http://pymolwiki.org/index.php/Get_raw_distances Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 _______________________________________________ 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
