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?
Rosetta discards and does not output much of the header information in the PDB files. If the display program you're using for visualization relies on the explicit annotation of secondary structure found in the PDB file, it will not display such structure info from Rosetta output files.
Most structure visualization tools (like PyMol and Chimera) have the ability to impute secondary structure from backbone geometry. Depending on the program, this may happen automatically, or there may be a command/tool you can invoke (e.g. "DSSP") to make this determination. I would recommend consulting the documentation for your viewing program, to see how to calculate/display secondary structure for PDB files without explicitly annotated secondary structure records.