clean_pdb.py

[Anonymous]

Hi guys,

I just installed Rosetta in my Mac and trying to do the ResettaCM following the tutorials (https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial). when i do the first step: Rosetta/demos/tutorials/rosetta_cm/scripts/clean_pdb.py 2RH1_ISOLATED A

I got this fault: rosetta/main/demos/tutorials/rosetta_cm/scripts/clean_pdb.py: /dors/meilerlab/apps/Linux2/x86_64/bin/python2.5: bad interpreter: No such file or directory

python in my mac is Python 3.6.8.

anyone know how to fix it?

Thanks!!

[Anonymous]

Hello, 

It looks like this script refers to a python executable that is only availabile if you are using the meilerlab’s setup. When you open the clean_pdb.py script in a text editor and change the first line to “#!/usr/bin/env python2” it should fix it.  If you wanna run in python3 you would need to change some print statements…etc 

Looking at the script it is also likely that you won’t have the amino_acids module installed.  I have attached a script that I think should fix these two issues. It would not let me upload a .py file so I changed the file extension to .txt. 

 

[Anonymous]

Hi Taylor,

I used your attached script and it is working well now.

Thank you so much. It means a lot to me.

Best wishes!

[Author]

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