Chimera's hydrogen bond counting tool (FindHBond) from command-line?
Hi all, Is there a way to run the Chimera's hydrogen bond counting tool (FindHBond) using the command line only? Could someone post me to the best way? -- Gustavo Seabra Professor Adjunto Universidade Federal de Pernambuco Recife - PE - Brasil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)
Hi Gustavo, There is a “findhbond” command (or “hbonds”, same thing) that has all the same options as the FindHBond graphical interface. Use command “help findhbond” to show the manual page for the command and its keywords, or see the same thing on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> Exactly how to give the command depends on all the options you want to use, and just like the dialog there are many possible options. If you enter just “findhbond” without any options, it will use defaults and all atoms. Another common use is to select some atoms and then use the command with the “selRestrict” option to find only the hbonds of those atoms. The following example includes display options to show all residues that have hbonds and make the lines thicker and color them orange. findhbond color orange linewidth 3 reveal true 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 1:47 AM, Gustavo Seabra <gustavo.seabra@ufpe.br> wrote:
Hi all, Is there a way to run the Chimera's hydrogen bond counting tool (FindHBond) using the command line only? Could someone post me to the best way?
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,
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Elaine Meng -
Gustavo Seabra