I am visualizing some molecules with Molden. Is there a way to hide hydrogens, without deleting the hydrogen entries from the structure file?
As long as you are not using an ancient version of Molden, this should be no problem. (The oldest one I found in my software archive was Moleden5.1 from January 2014 and it already contains this feature.)
In the Molden control window there is a button with an italic H. This will open a menu with "Excl. All Hydrogens", "Excl. H except H-bond", "(Re)calculate H-bond", "H-bond parameters", and "Opt. H positions". I'll leave it to you to play around with it, below you find a small animation of the first two modes for the base pair GC.
And because it is a little bit too tiny in the gif, here is a crop of the Molden control window.