Category Archives: PyMOL

PyMOL: Remove hydrogens and water

It took too long to find a proper solution on the web when searching for “pymol remove hydrogens” or “pymol remove water“. Therefore this short post.

For removing hydrogens, best use a selection:

remove (hydro)

There also is a special selection name available:

remove hydrogens

For removing water we can use a selection based on the residue name:

remove resn hoh

However, I most often use a more intelligent command for removing solvent in general:

remove solvent

Rename an object in PyMOL

Long time ago since my last blog post… maybe I should just write the small things down. For my PhD, I’m currently working with PyMOL and was wondering how to rename an object there. So I googled searched for “pymol rename object” and did not find the proper solution on the first page. But there is one. Maybe this post will show up for the next one searching for “pymol rename object”. Continue reading