What is the name of the darker blue/purple section that is cut out of the magenta molecule?

Basophils

Explanation:

Basophils are a special type of white blood cells that are produced in the bone marrow and their main role entails inducing and maintaining allergic conditions.

In staining, Basophils shows dark blue granules which contains histamine, heparin and peroxidase. In preparation of Schiff reagent; magenta molecule (Fuchsin dye); gives a range of colors from magenta to purple. The stain cause nuclei to become blue, and glycogen and fungi to become magenta in color.