In the Rosetta documentation, the description of options "-fix_natsc" and "-trim" are:
"- add -fix_natsc if you want to fix sidechain conformations from
the starting template structure to be fixed during the simulation. By
default, Rosetta will repack sidechains of loop neighbor residues."
"-trim: this will model loop conformations in the context of their
neighboring residues instead of the whole protein. Useful if
you are modeling short loops within a large template structure
sot that residues far away from the loops will be trimmed off
during the modeling and restored when final model is output."
My question is what is the precise range in terms of "neighbor residues"? Can we customize the range?
Thanks a lot!