Hi Prija, PyMOL does have trouble with heteroatoms every now and then. Is the structure public--if so, can we please have the PDB ID? It'll be easier for us to hunt for a solution if we have the data.
Cheers, -- Jason On Mon, Apr 18, 2011 at 5:45 PM, Prija Ponnan <prija.pon...@gmail.com> wrote: > Hello > I am trying to visualize a protein-ligand complex of a metalloprotein using > Pymol. > The ligand and certain amino acids are coordinated with the metal ions in > the binding site.The binding site also have some water molecules which are > also making interactions with amino acids and the metal ions. But using > Pymol i am not able to visualize the coordinated bonds. > When I am visualizing the binding site of this protein using Pymol, the > water molecules are showing multiple hydrogen bonds (6 hydrogen bonds), > which is not correct according to the valency of oxygen. > > Please help me > > Thanks > > > > > Prija Ponnan > > Research Student > Department of Chemistry > University of Delhi > Delhi-110007, India > & > Canadian Commonwealth Scholarship Program Scholar > College of Pharmacy and Nutrition > University of Saskatchewan > Saskatoon,SKN5C9,Canada > > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > 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 ------------------------------------------------------------------------------ Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev _______________________________________________ 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
