Most of this information concerns macromolecular (protein, DNA, etc.) rendering. Casual science lovers might not be so familiar with these types of programs, but making cool images of your favorite enzyme is ridiculously easy with the right tools.

Please feel free to add anything in the comments that might also be helpful to others if I've missed it.

Download source files

• RCSB Protein Data Bank This is where you'll download the actual crystallographic data you'll need for your macromolecule of interest. Each entry has its own unique 4-letter code, and these files are opened using any of the programs mentioned below. To download the file, click "Download Files" next to the 4-letter code and select "PDB File (Text)".

Some molecules will have multiple structures available. Quick example, alcohol dehydrogenase (ADH) has 236 total. Here's a few tips on how to sort through to find what you want:

Species - Of the 236 ADH entries, 43 are homo sapien.

Ligand(s) - What do you want bound to your structure? Entry 1ADC is ADH bound to ethanol, while entry 6ADH is ADH complexed w/NAD. Scroll about halfway down the page for each entry and you can see the ligand and its chemical structure.

Resolution - Some entries might be the same ligand bound to the same structure, but with differing resolutions. Resolution is given in angstroms, with lower values being higher resolution. If it's not given in the title, the entry will have it under Experimental Details.

Programs

• PyMOL This Python-based program is what the majority of scientists use for visualization. It has a ton of features that make it probably the most powerful out there, but new users should definitely spend some time familiarizing themselves with the different functions and layout.

Fortunately, PyMOL's ubiquitousness means there's loads of info and tutorials out there. Perhaps the most helpful resource is the PyMOL Wiki, which has a great article for beginners.

I've uploaded a couple of examples of what I've done using PyMOL that might give you an idea of what it can do beyond the usual ribbon diagrams:

apo-ferritin

simple DNA strand

There is another open-source program, Jmol, that is supposedly comparable to PyMOL. Although I have no personal experience with it, I've heard it is less feature-rich than PyMOL and it seems to have fewer tutorials/resources as well. Maybe someone else can comment on this or RasMol.

• QuteMol It doesn't get any easier than this. Interface is insanely simple, as this comes with a bunch of preset styles that are pretty cool. Things like lighting and depth can be adjusted, but this program is extremely limited in terms of customizability. Nevertheless, it takes seconds to use and gives pretty fun results. There's even a preset to give molecules a style similar to David Goodsell's work.

Here's the same DNA file as above, but processed in QuteMol. I spent no time adjusting these. I literally opened the file, hit a button for a preset and saved, then hit another preset and saved that.

DNA 1

DNA 2

That's all I've got for the moment. I'm sure I'll add more later, but feel free to submit anything helpful I might've missed.

I've made a simulation of the collision that is hypothesised to have formed the moon.

It's art, in the sense that its accuracy comes from having (vaguely) replicated other more accurate simulations, rather than because it is ab-initio expected to be correct.

But it is a simulation, and the stuff in the simulation does obey physical laws, even if not tuned perfectly.

The article is here:

http://www.articlesbyaphysicist.com/moonform.html