Dear Rajlakshmi Chetty,
To limit which H-bonds you are finding, first “select” some atoms like the ligand only, and then use the “Only find H-bonds...” option as shown in the dialog.  You have the option turned on, but you probably didn’t select any atoms first.  For explanation of that option and its further options, click the Help button on the dialog or see the same information here at our website:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

See also the “If endpoint hidden, show endpoint residue” option.

Selected atoms are shown with green outline.  There are many ways to select, such as  Ctrl-click on one ligand atom and then press keyboard up arrow to increase to all ligand atoms, or with a command, etc. as explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 7, 2018, at 12:15 AM, Rajlakshmi Chetty <rrlchetty2013@gmail.com> wrote:
>
> Dear Sir/Madam
>
> Greetings for the day!!
>
> Myself Rajlakshmi Chetty, is Doctoral student in field of Nanomaterials. I am self learning and using chimera since back few days with the help of website tutorials and am stuck with a problem which is described below:
>
> I have .pdb file format of docked complex (Hex software) in which their is H bond is missing between ligand and receptor when opened in chimera. I tried Tools>structure depiction>find H bond but in that parameters query when i apply I am getting H bond of the whole complex which I don't want. I want to visualize H bond or any bonding between ligand and receptor. Is their any other way or what parameters change i need to do?
>
> I have attached H bond parameters dialog box with this mail.
>
> This problem where I am stuck is need for the time for my research work. So your kind help will be a great blessings for me. Your help of gratitude will be highly appreciated.
>
> Thanking you and looking forward for your reply!!