I ran relax on a structure downloaded from pdb (after I cleaned it using PyRosetta's cleanATOM()), following the instructions here: https://www.rosettacommons.org/docs/latest/preparing-structures.html. The exact command I used is this:
-no_optH false \
-relax:ramp_constraints false \
This results in a new .pdb file, which I presume contains the relaxed structure, and a score file, "score.sc". This score file contains an entry "total_score", and I am wondering what it means. Is it the score of the relaxed structure? Or is it the delta-score associated with relaxing (score_relaxed - score_initial)?
To compare, I did a score.linuxgccrelease on the relaxed structure, which results in a new score file, default.sc. However, the score entry in this file is completely different from the "total_score" outputted by relax.
By the way, I am a newbie to rosetta. I appreciate your help.