On Wed, Sep 7, 2011 at 12:02 AM, Thomas Holder <spel...@users.sourceforge.net> wrote: > 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,
I will try. Thanks again for your help. > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > -- Best Regards, lina ------------------------------------------------------------------------------ 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
