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I am visualizing some molecules with Molden. Is there a way to hide hydrogens, without deleting the hydrogen entries from the structure file?

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    $\begingroup$ I don't see any such feature in the manual or command-line flags. Offhand, I'd say no. $\endgroup$ – Geoff Hutchison Jun 9 '15 at 16:57
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    $\begingroup$ @Geoff It has and had this option for a while at least. I checked the history and it came sometime in Molden3.2 (added a button "H" to undisplay hydrogens). $\endgroup$ – Martin - マーチン Nov 20 '17 at 14:33
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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.

screen capture of different display modes

And because it is a little bit too tiny in the gif, here is a crop of the Molden control window.

screenshot of Molden control window

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AFAIK there is no such an option in molden. Take another (free) program (f.e. molekel)

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    $\begingroup$ This is false (and likely was false at the time of answering), see my answer for how to do it. $\endgroup$ – Martin - マーチン Nov 20 '17 at 14:25

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