1 - What is the exact section of the 2GT0.pdb protein to be made on-site
2 - How do you open the 2GT0.pdb file on jmol
Replies are appreciated.
1. That information isn't public- you'll find out when you get to competition. The rules specifically say that you're modeling Oct4, though, and there's a bunch of other non-Oct4 stuff in the PDB file as well, so you know that you'll be modeling one of the Oct4 pieces (actually, the PDB file says Oct1. I'm not sure who's right, although I'd put my money behind the PDB. But that's what they're referring to).
2. Have you read the Protein Modeling Wiki
? If you read that and are still confused, what have you tried so far?
I modeled the zinc fingers, the DNA, and plan on modeling the sidechains on the helices that interact with the DNA. I just made little sidechains and wired them to the mini-toober. For the notecard, you just explain what creative additions you modeled and why they matter to the protein's function.
Thanks for your quick reply! How would you find which sidechains/helices interact with the DNA? Also, are there any materials that you recommend making the sidechains/DNA/zinc fingers/etc. out of?
I'd try researching the properties of specific sidechains (there might be a useful link on the wiki, I don't remember exactly), then showing in Jmol the ones that sound like they might interact with DNA well. If they are known to interact with other molecules and are in the right spot (i.e., in contact with the DNA), they probably are the ones that interact with the DNA.
I've had good results using pipe cleaners for sidechains; other useful materials (for sidechains, ligands, etc) include jewelry wire, Model Magic, cardboard, paper, and really just about any craft supply. My model is all supported by 22-gauge jewelry wire, because I make jewelry (or at least I did, before my protein model took over my beading table) and therefore have a lot of experience with what it can do; I typically use Model Magic for ligands, and my model is on a foamcore base. At the end of the competition season, I'll post pictures in the Image Gallery (I meant to do this with my hemagglutinin model from last year, but sadly it was damaged before I got a chance).
Also, the notecard needs to do two things: show what each addition is, and explain what each addition means. In other words, it needs to have a legend, just stating things like "purple pipe cleaners = histidine" or however you want to show it, and it also needs to have a paragraph that explains why you chose to show those histidines, or whatever it is that you focused on for your creative additions.