How to clean up atoms with bonds when some atoms are deleted

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1

Dear Everyone,

I was trying to insert some atoms inside water with “delete_atoms overlap”. The result is, some water molecules are deleted partially. Thus this error comes up: Bond atom missing in image check.

I am wondering how to clean up the atoms with broken bonds.
Thanks for any suggestions.

Best,

2

Dear Everyone,

I was trying to insert some atoms inside water with "delete_atoms
overlap". The result is, some water molecules are deleted partially. Thus
this error comes up: Bond atom missing in image check.

I am wondering how to clean up the atoms with broken bonds.

​try reading the whole documentation for "delete_atoms" again and check out
the "bond" keyword.​

​axel.​