"Current visualization software, such as UCSF ChimeraX6, can only render one or a few protein structures at the atomic level."

Lots of current visualization software is focused on visualizing a single protein structure (for example, ChimeraX). New visualizing and modeling systems are being developed to go up in scale to cellular scenes and even whole cells. For example, systems like le Muzic et al.'s CellView (2015) [1] are capable of rendering atomic resolution whole cell datasets like this in realtime: https://ccsb.scripps.edu/gallery/mycoplasma_model/

[1] : https://www.cg.tuwien.ac.at/research/publications/2015/cellV...