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Haddox / score_monomeric_designs

Computational pipeline for scoring protein designs using a variety of biophysical metrics
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External scripts in 'make_fragments.py' #18

Open GangyuSun opened 2 years ago

GangyuSun commented 2 years ago

Hi Haddox, I found that there are many scripts introduced by 'make_fragments.py' not existed in the folder. Is there any suggestion how can I get those external scripts? BTW, is there a script to calculate 'abego res profile' it seems very useful .Any help is appreciated! Sincerely Gangyu.

Haddox commented 2 years ago

Hi Gangyu,

Sorry for the delayed response! Good question about the make_fragments.py script. That has a complex set of dependencies that exists on the Baker lab server, but which were difficult to extract and put on GitHub. However, I know that a few labs have done this, and they might be able to help. For instance, Gabe Rocklin (http://www.rocklinlab.org/), who originally developed this pipeline, was able to set up his own version of make_fragments.py when he started his lab. So you might consider reaching out to him.

Also, it looks like abego_res_profile is computed in the script scriptis/enhance_scorefile.py. I did not write this script, and so do not know exactly how it is computed. But it should be possible to figure that out by looking closely at the script.

Hope that helps and let me know if you have any other questions!

Hugh