Executing the clean_pdb.py script

[Anonymous]

Hello All,

I am currently running RosettaCommons on linux and am attempting to run the clean_pdb.py script on my native protein.
As of now, I have changed it to an executable file as recommended, but I am unsure what the command is to run this script on a certain pdb.

As of now my command is $ python clean_pdb.py script path/to/pdb, but this doesnt appear to be correct. Can anyone direct me on what the script requires for a command and exactly what to type in so it runs it on my vinculin.pdb protein.

So for instance, my command would be,$ python clean_pdb.py home/downloads/vinculin.pdb but this is not working.

Thanks for your help,

Ralph.

[Anonymous]

Hi, would you like to try:

#For single chain output:
python /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/clean_pdb.py 4KMT L

#For multiple chain output:
python /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/clean_pdb.py 4KMT HL

Something maybe useful:
https://www.rosettacommons.org/node/3807#comment-7766

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