Deleting bonds in avogadro

[Steven_Wathen]

Hi,

Is there a way to delete a bond without also deleting atoms?

For instance, after I draw cyclohexane I decide I don’t want a ring after all. Can I break a bond to form hexane?
If I delete one of the carbon atoms, the ring will be broken, but I won’t have 6 carbons anymore.

Thanks,

Steve

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Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

[mhanwell]

On Wednesday 19 August 2009 20:12:17 Steven Wathen wrote:

Hi,

Is there a way to delete a bond without also deleting atoms?

For instance, after I draw cyclohexane I decide I don’t want a ring after
all. Can I break a bond to form hexane? If I delete one of the carbon
atoms, the ring will be broken, but I won’t have 6 carbons anymore.

Thanks,

Steve

Hi Steve,

You can right click on the bond and it should delete it. I think that is in
the tooltip for the draw tool, if not I should add it in.

Marcus

[VKuchenbecker]

Hi! Many years later, im using Avogadro2 1.100.
And i tried everything but still cant delete bond.
In fact, nothing happens if i right click bond with the tool, just works on atoms. Could someone help?

[ghutchis]

@VKuchenbecker

In fact, nothing happens if i right click bond with the tool, just works on atoms. Could someone help?

There was a bug reported recently (and since fixed in nightly builds) for deleting bonds with “adjust hydrogens” unchecked:

Issue: Draw Tool Doesn't Delete Bonds When "Adjust Hydrogens" is Unchecked

Issue: Draw Tool Doesn’t Delete Bonds When “Adjust Hydrogens” is Unchecked Environment Information Avogadro version: Avogadro 2 - 1.100.0 (Flatpak) QT version: 6.8.1 SSL version: OpenSSL 3.3.2.3 Operating system: Ubuntu 24.04 Expected Behavior The Draw Tool should delete bonds between atoms. Actual Behavior When the “Adjust Hydrogens” option is unchecked, the Draw Tool does not delete bonds between atoms. Steps to Reproduce Draw any molecule. Try to delete a bond using the Draw Tool while “…

Try a nightly build.

[VKuchenbecker]

I just did and the problem persist all the same. Without Adjust Hydrogens checked, it wont delete bond.
Im strugling with because it is essential for generation of ORCA NEB_TS coordinate files from TS search.

[ghutchis]

@VKuchenbecker

I just did and the problem persist all the same. Without Adjust Hydrogens checked, it wont delete bond.

I can assure you that the logic in HEAD is correct and it tests. It’s possible that the nightly build has not updated

Can you explain why you need to change bonds for the ORCA NEB? I thought you just needed atomic coordinates? (I know what’s in the ORCA manual, but the input file itself has no bonds.)

Or put another way … what are you trying to set up for the NEB calculation? As far as ORCA is concerned (i.e., via XYZ files) all you need are atoms. You can leave the bond depiction in Avogadro even if you stretch it beyond reality: