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I am using Avogadro for visualizing some cluster systems. Is there a way to hide the bonds of the system, ie. only showing atoms?

Thanks!

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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.

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Actually, it's not too hard. One of the display types in Avogadro is "van der Waals" which will just show atoms - no bonds. So you'd enable the vdW display type and then turn off the "balls and sticks" one.

Yes, you could write code which removes bonds, but why?

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  • $\begingroup$ The vdW display settings is a space filling model. I believe the OP just wants the ball&stick model without the sticks. $\endgroup$ – Martin - マーチン Sep 12 '14 at 2:24
  • $\begingroup$ @Martin Obviously that should have been a comment for the OP. However, the description of "cluster systems" makes me believe vdW might be just fine. (For example, I solely use vdW in rendering inorganic crystals.) $\endgroup$ – Geoff Hutchison Sep 12 '14 at 13:34
  • $\begingroup$ You are right, I did think too much about molecules. For example if you have molecules that make up a cluster you barely see anything anymore, because atoms become too big, but then you could still use ball&stick modus. $\endgroup$ – Martin - マーチン Sep 12 '14 at 13:37
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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 .xyz using 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!

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  • $\begingroup$ As far as I know, avogadro uses babel conversion internally. You will have to change the bond values, no matter if there is any bond information in the file format. Avogadro will draw bonds based on the default values. $\endgroup$ – Martin - マーチン Sep 12 '14 at 2:23
  • $\begingroup$ Indeed, this will not work. Saving as .xyz will only remove the bonding information in the file. They will be re-perceived by Open Babel upon import. That's not what the OP wants to do. $\endgroup$ – Geoff Hutchison Sep 12 '14 at 14:39

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