I am new to using Avogadro, but I’ve made a molecule and I want to shift origin to one of the atoms in the molecule. Should be pretty easy, except the Cartesian editor doesn’t label the atoms it only says they are a carbon, oxygen, hydrogen, etc. Is there any way to figure out which atom is which using tools in Avogadro or will I have to just spend the time figuring out what position vectors go with each atom?
You could turn on the “Labels” option, which by default should set the atom indexes on each atom. Then it’s pretty easy to figure out the order in the Cartesian Editor.
But easier than that, you can use the Align Tool to do this. The first atom you click will be translated to the origin. The second atom you click will be aligned along the specified (x, y, or z) axis.