Glycan minimization – Rosetta Commons

This topic has 3 replies, 2 voices, and was last updated 8 years, 3 months ago by Anonymous.

Viewing 3 reply threads

Author

Posts
- October 6, 2016 at 8:51 pm #2520
  Anonymous
  Hello,
  
  I am currently attempting to minimize an antibody that has already been glycosylated. Does pyrosetta minimize glycans in the structure?
- October 6, 2016 at 9:05 pm #11924
  Anonymous
  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).
  
  ~Labonte
- October 6, 2016 at 9:05 pm #12445
  Anonymous
  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).
  
  ~Labonte
- October 6, 2016 at 9:05 pm #12966
  Anonymous
  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).
  
  ~Labonte
Author

Posts

Viewing 3 reply threads

You must be logged in to reply to this topic.