I am currently attempting to minimize an antibody that has already been glycosylated. Does pyrosetta minimize glycans in the structure?
Yes, if you use the correct flags and if the glycan successfully loads.
For the 1st "if", you need to use the -include_sugars flag. (To load flags in PyRosetta, pass them as a string to the init() function, e.g., "init("-include_sugars")".
The second issue is trickier. Because the majority of .pdb stuctures have errors in how they record sugars, it rarely works out of the box. First, you will need the flag "-alternate_3_letter_codes pdb_sugar". You may run into some naming or connectivity issues. If you do, please contact me directly at <JWLabonte@jhu.edu>.
Everything involving sugars is basically in beta.
Also, if you have a branched glycan that you wish to minimize, you will need a MoveMap with set_branches(True).