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