I am attempting to use the rosetta FixedBB design application to investigate possible conformation changes that may occur given a single point mutation whilst taking into account romaters. However, as an initial run of the application I do not change any residues or rotamers as I just want to see how this application works, but the resulting output differs from the input structure in that the beta sheets are not visible when visualized.
The residue file only contained NATRO and the command used to run the appliation was PATH_to_rosetta_main/source/bin/fixbb.default.linuxgccrelease -in:file:s 1qlx.pdb -resfile resfile.txt -out:suffix _resout_none > log_resout_none.txt &
The same situation also applies when I run the simpleThreadingMover, where the beta sheets are missing from the output structure.
Is there perhaps some underlying implementation that has defaults which might cause this?