I am trying to score how well different protein models fit into one electron desity map. I have tried using the score_jd2 tool with the flags:
"-database /programs/PDB/rosetta-3.13/main/database -in:file:s ./structures/*.pdb -edensity:mapfile ./emd_12705.map -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"
This program returns a score file where one of the columns is named as "elec_dens_fast", which I thought could correspond to how well is each structure fitting in the map. However, the structure with the lower value in this column then has a really high energy score in the "total_score" column. And when I look at the pdb structure of the model using pymol I can clearly see how it is not the one that better fits into my electron density map. Then, what do "total_score" and "elec_dens_fast" mean? And how do I manage to measure the fitness of my models to the map?