I hope this message finds you well. I would like to use the InterfaceAnalyzerMover to determine the seperated interface energy difference between three or four chains. I noticed in the metadata page for InterfaceAnalyzer there are two flags to accomplish this (link). However, I could not find these flags in the PyRosetta 4.0 documentation describing InterfaceAnalyzerMover, and I am not sure how you would use these flags in Python (link).
These are the flags I am looking for (link):
"-interface (string) - Multichain option. Which chains define the interface? example -interface LH_A to get the interface between chain groups LH and A. Works for sub interfaces such as L_H by ignoring any chains not specified in calculations. Not tested thoroughly beyond three chains.
-fixedchains (string) - Multichain option. Which chains are in the two groups to define the interface? example: -fixedchains A B to keep chains A and B together, and C separate, out of a pose that contains A, B, and C. Note a space between A and B. Analogous to -interface option. Includes all chains of the pose. Not tested thoroughly beyond three chains."
On a separate note, I noticed ref2015 is the default scoring function. Is this still the preferred scoring function for determining binding affinity? If not, what would be the best way to change it?
Also, I noticed there is a set_pack_rounds() function, and the default is one round of packing. How can I know if this is enough?
I have attached the code I am running, as it is now below, in case that is helpful. Please let me know your thoughts when you have time.
#Get PDB file pose = pose_from_pdb("name.pdb") #Run InterfaceAnalyzerMover ia = pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover() ia.set_pack_input(True) ia.set_pack_separated(True) ia.set_use_tracer(True) ia.apply(pose)