Why is the POSE_ENERGIES_TABLE always appended to Rosetta pdb output files by default?
Is there an output flag to toggle this behavior on or off?
I have the same concern (I asked it here: https://www.rosettacommons.org/comment/8281#comment-8281). These energy tables sometimes double the size of the pdb files, which is not good.
I looked through the code base to see if there was anyway to do this. Currently the pose is tied to the score table so they both get dumped to the PDB file by the job distributor. If you are looking to reduce file size, you could pass -out:pdb_gz to zip the output files before you parse them. Alternatively you could look into silent files that can greatly reduce the file size and can be manipulated by many downstream rosetta applications. Can you comment a little further on the end goal and I can help find a solution?
I am just using the score app to clean and renumber the pdb structures. Right now I am using large datasets of pdb files to validate some protocols, so the large size of files is an inconvenience.
Sounds like a job for Rosetta tools rather than the apps. If you just want to do PDB manipulations and prepare them for Rosetta, checkout the tools directory that comes with Rosetta. Inside is two scripts for exactly what you are talking about. python tools/renumber_pdb.py and python tools/protein_tools/scripts/clean_pdb.py
Clean_pdb.py is really nice because it prepares the structure for Rosetta and can automatically pull it from the PDB if you don't have the file.