How does one create 3D structures like those produced by Ben Mills?

On Wikimedia Commons Ben Mills has produced several 3D ball-and-stick models (e.g., see (R)-thalidomide's structure which is also the first file attached) that I would like to be able to create too, he gave some instructions here but seeing how he last edited this guide over 6 years ago and I have tried and failed to follow his instructions with the latest version, I'm guessing because his guide is out-of-date. I am especially interested as to the cosmetic formatting he did, I know how to load molecules in DS Visualizer but I do not know how to get the colours Ben Mills used, or how to show delocalized charges along the phenyl rings. The second attached image is my best attempt to date at mimicking Ben Mills' 3D model.