In Jmol, I know that there's backbone, wireframe, and spacefill modes, but the proteins look different when you first open a file (like the pictures here
). What is this called?
Also, which display mode is the best to use when modeling the protein?
EDIT: just read that the model must be based off the "alpha carbon backbone display", so I guess that answers my second question.
That's the "ribbon" display mode (or something like that, I've used it in other protein visualization software but since I only use Jmol for SciO, it's not the most useful mode for me in Jmol). It shows secondary structure- alpha-helices as, well, helices, and beta-sheets with arrows.
This information is on the Protein Modeling Wiki
, but you should use backbone for the whole thing (as per the rules), probably wireframe for any sidechains you choose to show, and spacefill for ions.
New question: what are the crosslinkers that came in the prebuild kit for? I don't find any mention of them in the wiki or the MSOE videos.
The crosslinkers are just for increasing the structural stability of your model. They don't represent any particular structure, although I suppose you could
use them to represent disulfide bonds or something similar. They end up being a few Angstroms long to scale, so it's within the plausible range for such a bond. But again, they don't represent anything unless you say they do on your card.