Results during evaluationare ordered based on system sorting and could give different results depending on the specific system settings.

[JanAarts]

Results are evaluated based on the system sorting of the merged directory. In calculate_rmsd_all.py line 253-255:
if decoy_dir.exists(): decoys = list(decoy_dir.glob("*.pdb")) # Collect all PDB files in the "merged" directory model_dict[model_identifier] = decoys

Should be changed such that the models are sorted numerically. For example like instead of line 254:

import re files = sorted( decoy_dir.glob("*.pdb"), key=lambda p: int(re.search(r"\d+", p.stem).group()) )