Just a quick question. I am running a few (thousand) structures through score_jd2 using the command below, and I am occasionally seeing this message I've never seen before:
No structure mods allowed during scoring!
Any idea how this would be tripped? Some of these structures may have missing atoms and need some rebuilding of side chains during pose construction, but shouldn't that occur before scoring? The structures themselves look fine, and can be loaded into PyRosetta with no issues.
score_jd2.linuxclangrelease -database $ROSETTA3/database -no_output -l ../PyIgClassify/DBOUT/renumbered_pdbs/PDBLIST.txt -ignore_unrecognized_res -ignore_waters -ignore_zero_occupancy false