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.
What is the error message that you are getting?
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.)
The Mac I use have Python version 2.7.