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 <[email protected]> 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 ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] >
------------------------------------------------------------------------------
_______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
