Hi Gustavo, Ah yes, my answer was for the Chimera command line. For the system command line, you can run Chimera in nogui mode with input python or chimera-command scripts. You could run findhbond with a chimera-command script, but you probably want to use a python script instead to also save the contents of the Reply Log to a file. To run in nogui mode you use the “nogui” startup option <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html> e.g. like this user posted <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002359.html> Here is information on how to run Chimera commands and save Reply Log contents in a python script. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 Apr 9, 2018, at 9:50 AM, Gustavo Seabra <gustavo.seabra@ufpe.br> wrote:
Hi Elaine, Thank you very much. However, it seems to me that the example you sent is supposed to be used in Chimera's command line, right? I was actually looking for a command I could issue from a shell command line, e.g. from bash, to create the list of hbonds without the need to start the GUI. Is there a way to do that? (More precisely, I want to use this command in a pipeline, using KNIME command line node to call it, and then treat the output in sequence.) Thanks,