Hi Lina, > Hope you won't mind this email sent to you directly.
not at all, that made it finally clear what you actually want! > Here I attached the pdb, > > which I want to add the aromatic H, > > The cur_1.pdb: only polar H was added. > > while cur_11.pdb I used h_add (selection of aromatic atom, namely C3, > C5, C6, C16, C17, C20) > > I only kept one H here, and removed another. PyMOL only knows bond valences for known amino acids, but your file contains a molecule which is not a protein. You can either explicitly define which bonds are aromatic or double bonds, or PyMOL can guess for you from geometry. # load molecule without hydrogens load cur_1.pdb remove hydro # show double-bonds in line or stick representation set valence # make rings aromatic and C=O double bonds valence guess, all, all # add hydrogens h_add all If it does not work to guess valences, you need explicit statements: # select rings select ring1, name C2+C3+C4+C5+C6+C7 select ring2, name C15+C16+C17+C18+C19+C20 # make rings aromatic valence aromatic, ring1, ring1 valence aromatic, ring2, ring2 # define double bonds valence 2, name C10, name O3 valence 2, name C12, name O4 Hope that helps, Cheers, Thomas -- Thomas Holder MPI for Developmental Biology ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ 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
