I am trying the tutorial of Comparative Modeling using Rosetta and I am not able to run this script (<path-to-Rosetta>/Rosetta/demos/tutotial/rosetta_cm/scripts/clean_pdb.py 2RH1_ISOLATED A). The “path-to-rosetta” in my Mac is “Applications” and also I have the latest python version. Does the scripting change with python versions as well?? Any help in this regard is greatly appreciated.
The error message I get is “Directory not found”. But I found this Nat Protocol paper (Combs SA et al. 2013) where they use the following script (highligted in black)- /Applications/rosetta_bin_mac_2017.08.59291_bundle/tools/protein_tools/scripts/clean_pdb.py 2RH1_ISOLATED.pdb A So the “protein_tools” was missing from the tutorial script.
Re: “latest python version” — note that many of the Python scripts in Rosetta are written for Python2, not Python3, so you may need to run them with `python2.7` rather than `python3.6`.
(If your OS is one of the few which flouts the Python standard and aliases plain `python` to a Python3 version, you may need to explcitly reference `python2.7` rather than plain `python`. — I don’t think this is the case for Macs, though.)
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