Hi Farzaneh - Are you looking for something programmatic to use for many different structures, or just analyzing a single structure?
With just one structure (or a few) you can do most of this using the GUI by eye. 1. To find the length of each H-bond involving your ligand, (let's say the object or selection is called "my_ligand"), click "S (show) > Labels" for the 'my_ligand_polar_conts' object that was created when finding the H-bonds. 2. To see which kinds of residues are involved, you can type on the PyMOL command line: `show sticks, byres (my_ligand within 4)` which will show sticks for the entire residue (byres) of any residue with any atom within 4 Å of my_ligand. 3. For the number of H-bonds in an individual active site, you can probably just count them by eye. Alternatively, if you need a more automated approach, have a look at Thomas Holder's Polarpairs plugin: http://www.pymolwiki.org/index.php/Polarpairs Hope that helps. Cheers, Jared On Aug 23, 2016, at 2:39 AM, Farzaneh Namazifar <f.namazifar706...@gmail.com<mailto:f.namazifar706...@gmail.com>> wrote: Hi Dear all; I am a PyMol user. I read the PyMOL tutorial<http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/index.php> about the hydrogen bond. I need some informations about hydrogen bond like: 1- length of hydrogen bond between two residue 2- which kind of residues are in the hydrogen bond 3- Number of hydrogen bond in active site As above, I need informations about Hydrophobicity of residues in the active site. and else information about pi-pi interaction in DNA... I need your help ... Best Regards. Thank you in advance. ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto: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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