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We know that bonds, per se, are only characterized after topological studies but their visualizations is an easy and fast way to see if there are "connections" between some particles.

I tested visualizations software like Jmol, Chimera, Maestro, VESTA, Ovito, Avogadro and VMD and each one is displaying the bonds in a different way.

As a test, here is a small system of Ni atoms:

4
 energy: -19.116588819886 gnorm: 0.000358126128 xtb: 6.5.1 (863dcdc)
Ni           4.15720993928297       23.06900153804784        8.00195919232334
Ni           2.44935450390468       21.62046788970323        7.87888994741951
Ni           5.58700274720514       21.36098908827675        8.26402186547672
Ni           3.87913280960721       19.91244148397218        8.14092899478043

The pictures below are the graphical representation in each of the software mentioned above.

The question: Which is the best way to display bonds? (or Which software is better representing the bonds for this system?)

Jmol:
Chimera:
Maestro:
VESTA:
Ovito:
Avogadro:
VMD:

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    $\begingroup$ In vesta and ovito, there is option to add bond where specific radius of interaction is required. $\endgroup$ Jan 20, 2023 at 17:13
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    $\begingroup$ Yes, all of these programs use some semiempirical rules to determine whether there is a bond between the atoms or not. Jmol and Chimera link all atoms; Vesta, Ovito and VMD appear to link none. It's all a matter of how you define a bond - which is a highly nontrivial question in general. $\endgroup$ Jan 22, 2023 at 18:12

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