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I am following the protein design steps presented in the Dr Mieler lab. One of the steps is to generate resfile with script. I checked my rosetta/tools/protein tools/scripts path, but there is not such a file. Where can I find this script?

Thank you

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Mon, 2020-10-26 19:42

The script isn't distributed with Rosetta itself, instead, it's distributed with the Meiler Lab protein design tutorial as a helper script. (It should be included in the scripts/ directory of the materials zip file for the protein_design tutorial.)


Mon, 2020-10-26 19:52

it seems like those scripts are outdated and do not work with python3 anymore :( 

Are there workaround tools for that? Also If I want to define interface beyoned the tutorial for my own project, how can I do that? 



Mon, 2023-05-08 15:24

We haven't gotten around to updating those scripts yet, sorry.

If you have Conda (or something similar), you should be able to make a new environment which is based on python2.7, which you can activate for those scripts specifically.

Alternatively, those scripts are just helper scripts. You certainly could just skip the script entirely and manually write the resfile instead. There's nothing particularly special about the script, it just autodetermines the residues which are in the interface for you. If you know which residues in your protein you consider to be interface should be easy to create the resfile manually.  The resfile syntax is relatively straightforward, so you should be able to create it in a text editor once you have your list of interface residues. (Or even generate it automatically, with your own script.)

Tue, 2023-05-09 15:32