I'm wondering if there is a software that helps to make an animated organic mechanism and show how arrows go. It would be clearer in visualizations.

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    You can use Jmol but you need to have the raw data from your animation; this usually comes from molecular modelling. I use GAMESS (US) for this work. But from your question, it isn't clear whether or not this is what you mean. – user1945827 Dec 6 at 14:57

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