Hole diagram

GROMACS version:2020.2
GROMACS modification: Yes

Dear users;

I’m working on a channel protein, I’d like to make a graph like Figure 3(a) in this paper;
The Cryo-EM structure of pannexin 1 reveals unique motifs for ion selection and inhibition | eLife (elifesciences.org)

I think this is what you call “Hole diagram”, do anyone know how to plot such kind of graph with GROMACS?
Please tell me which command I should use, and how can I do that.


HOLE is an external program used for visualization and analysis of channel pores. See the docs here:


Dear jlottammer,
Thank you for your reply. I’ll check it :)