I'm very new to protein modeling work, but from my understanding IgG1 Fcs have a glycan between the CH2 and CH3 domains. I downloaded an IgG1 Fc from the pdb database, but I can't seem to see where it is visually. What does it look like and if I open up the pdb as a text file, what symbol would it be and how would I locate it? Also if I'm doing homology modeling with one as a template, would I have to later add in the Glycan after the model is produced? If so how would I do that?
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Glycans are usually too flexible to be present in crystal structures. You probably can't see it because it's probably not there. If PyMOL or whatever visualizer you used didn't show it, it's very nearly certainly not there in the file. If you want to look in the file directly for it, it will be ATOM or HETATM lines whose residue type column isn't an amino acid, or water, or something else easy to identify; probably near the end.
Although we have a few developers working on carbohydrates, broadly speaking Rosetta (and every other modeling program) ignore their existence. Homology modeling expects them to NOT exist, and will be much harder to run if they DO exist. Generally proteins fold before glycosylation anyway so it's not going to be an issue for homology modeling most of the time.
As Steven said, most of the time we just ignore them. They are usually very flexible, and so do not resolve very well in crystal structures. Some structures may have pieces of the glycans. The base, etc. Some new EM methods are actually starting to show better glycan density as well as a more dynamic picture of entire glycan structures.
If you are interested in the glycans for some reason (once you start thinking about them from a structural standpoint, they can become extremely important), as Steven said, a few of us are developing glycan-specific code, applications, and rosetta script components in Rosetta. These include tools for actually glycosylating a pose with a glycan, modeling the glycans, and everything in between. We are not yet ready for prime-time, but sometime within the next 6 months we hope to be ready to go and published. I'm actually writing a lot of the documentation for it today. If you have a specific project you would like to collaborate on, we may be able to help - just email me (jadolfbr@gmail.com) or Jason (JWLabonte@jhu.edu). We could do a bit with what we have that may be of some use now.
-Jared