How to make most use of Animation tool and Align tool. I dont see any effect, i think iam not knowing to use it the right way.
Let’s take the align tool first. It’s intended to shift and rotate a molecule into a standard frame of reference (e.g, one specific atom at the origin, another projected along the x, y, or z axis):
This makes it easier for certain kinds of calculations (e.g., applying an electric field) or copy / paste to merge systems. For example, projecting a molecule along the z-axis and then inserting above a surface:
The animation tool (in Avogadro 1.9x / Avogadro2 betas) functions like the animation window in previous versions. It’s designed to animate trajectories or files with multiple coordinate sets (e.g., molecular dynamics).