I was referring to molecular assemblers - a machine that runs in a vacuum chamber at a controlled temperature. It receives through plumbing hundreds of 'feedstock gases' that are pure gases of specific type. It can make many (thousands+) of nanoscale parts, and then combine those parts into assemblies, and combine those assemblies etc.

Everything is made of the same limited library of parts, but they can be combined many different ways.

This makes possible things like cuboidal metal "cells" that are robotic, do not operate in water, and can in turn interact with each other to form larger machines, making possible something like the 'T-1000' from terminator 2. (it probably couldn't reconfigure itself as quick as the machine in the movie, but that doesn't matter since it wouldn't miss when shooting)

custom proteins are for medicine, and won't work at all the same way.