Hi Amali, PyMOL has parameters like h_bond_max_angle that are defined in terms of aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to guess the position of hydrogens.
If you need to add hydrogens you can use PyMOL’s h_add <http://pymolwiki.org/index.php/H_Add> command, alternatively you can use openbabel <http://openbabel.org/wiki/Main_Page>. Cheers, Osvaldo. On Sat, Nov 7, 2015 at 2:33 AM, Amali Guruge <amaligg2...@gmail.com> wrote: Dear All, > > My question is related to find the polar contacts between an enzyme and > ligand. I want to know when we find polar contacts, > > 1) protein should contain H atoms or not? > > 2) ligand molecule should contain all H atoms or not > > Please can anyone help me. > > Thank you in advance. > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 >
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