I have a question about KIC protocol. I am using the next generation protocol together with fragments. I think it should be fine but I just wanted ti double check couple of things.
Firstly, can I use fragments together with these flags? :
I am just checking that there isnt some kind of "conflict of interest" between using these flags as well as the fragments.
Secondly, the flag -loops:fix_natsc, does it just stop Rosetta remodelling the side chains of neigbouring residues? Not the actual loop residues?
And finally, when I am generating fragments, am I suppose to submit the full protein seqeuence to the Robetta or just the residues that are found within the loops?
Thank you so much! I am really gratefull for your help
My full flas file:
-loops:frag_sizes 9 3 1
-loops:frag_files /d/as12/u/sl002/rosett/run/loop/run_1/9mers.txt /d/as12/u/sl002/rosett/run/loop/run_1/3mers.txt none