# Comparative Modeling Tutorial Script not working

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Comparative Modeling Tutorial Script not working
#1

Hi All,

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.

Thanks

Srinivasan Krishnan

Post Situation:
Thu, 2017-09-21 12:00
Srinivas23

What is the error message that you are getting?

Sun, 2017-10-08 18:47
jkleman

Hi,

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.

Srinivasan

Tue, 2017-10-24 10:56
Srinivas23

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.)

Tue, 2017-10-10 09:22
rmoretti

Hi,

The Mac I use have Python version 2.7.

Tue, 2017-10-24 10:58
Srinivas23