I am using Avogadro for visualizing some cluster systems. Is there a way to hide the bonds of the system, ie. only showing atoms?
Not in the current version, as far as I know.
If you need it, you could either make a feature request on the Sourceforge page, or you could do something with extensions, such as making a new version of the ball and stick renderer removing the code that renders bonds, or making an extension that adds a button to delete all the bonds.
This is a minor comment, but I don't have the reps for it. (Any mods prepared to change this into a comment?)
One possibility is to convert the structure file to
babel and re-loading it in Avogadro, if the bond information is to be removed deeply. Otherwise adjusting the bond and atom radii should be able to make the bonds unobtrusive!