Dear Leila, You can see the help for the findhbond command by using the command: help findhbond We wrote this help so that it would not be necessary to ask how to do everything. Below is a short example, but please see the help for the many options, because what is “best” depends on what you want (color, output file, etc.) -- that's why they are options! select #0 findhbond selrestrict #1 log true line 2 color orange If you didn’t know what command was the same as the FIndHBond GUI, you could find out by clicking the Help button on the FindHBond dialog. Its help mentions that the related command is “findhbond” or “hbonds”. You can also search the help pages using Chimera menu: Help… Search Documentation. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 27, 2015, at 8:20 AM, leila karami <karami.leila1@gmail.com> wrote:

Dear chimera users

I have 2 models in my system (#0 for protein and #1 for ligand).

I want to use hbonds command for showing the hydrogen bonds between #0 and #1 models? (I know how to do this using FindHBond, but I want to know related command).

What is the best options for hbonds command to get above state?

Best, Leila