I sent a few suggestions in, having time to think about them, I would like to elaborate.
Do not make it hard for people to do things that they already know how to do, there are standards for this stuff that most people know.
All colours should be user definable, it should be like this, open colour settings -> show a picture of all the possible elements (lock colour, clash colour, hydrophobic colour etc...) click on the element you would like to change the colour of and bring up the palette, including the gradient (so a start and end colour) that you now have for an amino acid placement.
Make all of the key user definable, it may not make sense to you but A/D (translate / strafe) and W/S (zoom, go forward/backward) while using the mouse to rotate (while left clicking the background) will make a lot of sense to gamers. I also would say that A/Z (zoom, go forward/backward) will also make sense to gamers, it depends on the type of games they like (that's why it should be definable).
The mouse wheel needs to zoom as default.
Though of course the mouse need to be configurable too, such as the mouse wheel will select different tools (just like most FPS the mouse wheel changes the weapon) a quick pop up (that should be able to be toggled on/off) should tell the player what tool they have just selected and also remind them of what the short cut key is (not the default, but what the currently selected short cut key is). That may not make sense so let me explain, if I choose to use the W/S keys to zoom then I can use the mouse wheel to change tools.
Your suggestion and chat need to have all of the usual features, as I said in the suggestion, it's annoying not to be able to cut, copy, paste etc...
Hints should be able to be toggled on/off.
None of this is hard to do, it's just polish.
Have a happy new year and my best wishes to all.
I'm not going to add in the returns that were there before I pasted, I have to go and tie a load on a ute so catch ya all later Hugo be safe.