hi, all,
my question: if I want to model a loop of a protein, should I make fragment library for the whole protein, or just the part of loop?
How the rosetta program read the fragment files? For example, my loop starts from 200 to 215 of a 500-aa protein, if making fragment for whole protein, the "position" in fragment file for this loop is "position 200", while making fragment only for the loop, the position is 1. How the program read the position of loop?
Jarod
You will make your life a lot easier if you create fragments for the whole protein rather than just the loop. It's possible to use fragments for only the loop, but you'll have to edit and recompile the code to do it.
Thank you.
I also think generating fragment for whole protein is reasonable, but in the scripts of rosetta_antibody, I find that it only generate the fragment for H3 loop. Maybe the authors changed the codes to read fragment files.
Another question, for light and heavy chains of antibody, if I want to generate fragments for antibody, how should I do? Make fragment for light chain and heavy chain separately? Is there way to merge fragment files of different chains?
> hi, all,
> my question: if I want to model a loop of a protein, should I make fragment library for the whole protein, or just the part of loop?
> How the rosetta program read the fragment files? For example, my loop starts from 200 to 215 of a 500-aa protein, if making fragment for whole protein, the "position" in fragment file for this loop is "position 200", while making fragment only for the loop, the position is 1. How the program read the position of loop?
>
> Jarod