First, I recommend trying to use the command prompt. It's a little more difficult, but you have much more control over the display of your protein. If you're using Jmol online, the command line is right there under the display; if you have Jmol downloaded, you can access the command line by going to File -> Output Console.I've been using the menus to try to figure out what those (the molecules) are and which creative additions to add. I still don't really understand Jmol, so I'm trying to avoid messing around and confusing myself further, and we don't have our mini-toobers yet, so I can't really do much now, but I'm trying to start with figuring out the sidechains.When you first open a file in Jmol, it shows you all the atoms of the protein in "ball-and-stick" format. The spheres are individual atoms; red ones are oxygen in the default color scheme.I was wondering... on the Jmol of 2wbu, what are the red sphere things? Are they hydrogen molecules or something? I looked up the structure and found the alpha helixes and sidechains, but I just can't figure out what the little spheres are.
Have you been using the menus in Jmol or the command prompt? (That is, have you been changing the way you view the molecule at all, and if so, how?)
For anyone new to the event, I recommend reading the Protein Modeling Wiki; if you have more questions after reading that (which you most probably will), come back and ask (this also helps us keep updating the wiki to make it as helpful as possible).
Start by putting the entire protein in backbone mode by typing:
Now you have essentially a clean slate, with none of the sidechains showing- just the protein and the DNA (you don't have to model the DNA, but it's a good creative addition, so it can be useful to know where it is). In order to display a certain sidechain, you have to select it, and then choose a viewing mode- typically wireframe:
select [residue #] and sidechain
If you want to display all the sidechains of a given type, you can instead select the residue type; for example, if you wanted to select all the cysteines, you would use the commands:
select cys and sidechain
If you're wondering which sidechains to model, try looking through the links at the bottom of the Protein Modeling Wiki. One of the useful links is broken at the moment, but I'm trying to get that figured out. There are still some good resources there, though.