I came across the clustering.py script from the rosetta-3.5/rosetta_tools/protein_tools/scripts/ directory. As many other scripts within the scripts directory, that one depends on the rosettautil module found one directory up (protein_tools). When I run the clustering.py script it fails with an ImportError message stating that the rosettautil modules (.rosetta and .util in my case) cannot be found. Although I can make the script work by simply copying the whole rosettautil directory into the scripts directory, the whole procedure makes me feel uneasy. Is there a better way of doing this? Is this ImportError a known limitation of the current install or is it a bug?