Hi Kloe, I mentioned the FindHBond tool in my previous reply to you. Did you try it? <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html>
Open tools from the Chimera Tools menu, for example:
Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts
If you show a tool and click the Help button on that tool, it will explain the options. Also, you should go through the “Structure Analysis and Comparison” tutorial, which includes FIndHBond and some other things for looking at ligand-receptor interactions <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 29, 2018, at 3:43 PM, kloe brathon <kloebrathon@yahoo.com> wrote:
Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards, Kloe