The InterfaceAnalyzer documentation leads me to think that resfiles are fully supported for design purposes. However InterfaceAnalyzer does not seem to recognize my resfile. The structure output is identical to the input. Here is my protocol
1 C PIKAA A
2 C PIKAA A
Thanks in advance
InterfaceAnalyzer only analyzes the existing interface. The resfile option is there to allow you to override/alter the autodetection of which residues are IN the interface for packing purposes; it won't do design.
If you want to analyze the interface with different sequences, run it through fixbb first to generate the pose with the other sequence, then run it through InterfaceAnalzyer.
It is worth noting that InterfaceAnalyzer was never built to be a standalone application. It was built to be used inside other Rosetta protocols, so giving it the ability to mutate the sequence would be out of place. That's why it doesn't have that ability. I'll tweak the documentation to note it doesn't do design, thanks for pointing it out.