Have you ever thought to yourself “this is the most confusing thing I’ve ever
thought about, and I wish I could move it around in 3D?” No?
Well, apparently some researchers did at some point, because VMD allows you to
rotate the system and zoom in on specific parts.
They also enabled something called hot keys.
Pressing r on the keyboard will either start or stop a system from rotating
along the y-axis (get it, r for rotate?).
Pressing t allows the system to be translated (get it, t for translate?).
This means that you can move it around the screen (which is especially helpful
if you’ve zoomed in by scrolling).
Sometimes in VMD there are also some weird looking half in and out bonds
(or times it just looks like your system is broken in that specific view).
That can be fixed by pressing t, right-clicking with the mouse, and dragging
downward.
There are some other hot keys that you can read about in the VMD User’s Guide, but these will at least get you to stop asking yourself why the heck your protein won’t stop spinning.