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Fragment Insertion to Generate a Loop

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Fragment Insertion to Generate a Loop

Hello master builders/users,

I have a problem that I am encountering in my script that I (desperately) need some assistance with.   I am trying to generate Loops for a protein 4115 via fragment insertion method. I have attached my script for reference.

Here is what  am tryiing to acheive: 

insert Robetta generated fragments into structure and then refine the areas as loops. I want to perform more than a 1000 fragment insertions though if possible. I also want scores for the structures based on the starting structure (if possible). After looking at the pyrosetta manual, I was able to come to the conclusion that fragment insertion is only possible if you have a pose of a fragment so I tried to use dump pdb and fragment index together to no use. Then I tried using my own scripit with randomly generated sequences followed by pose generations, insertions and one cycle of refinement so that I can have scores available. But my script defiinitely has problems since the loop is not closing and I would rather be usinig fragments from robetta generated fragments. Also how can I write it so that I can have one script doing all insertions?

 I would really appreciate a quick response!!!!

P.S. after refinement the .fasc file contains an rmsd. Is the value based on the comparison between the structure before and after refinement? Also, instead of usinig random number generator for files, can I use any function from pyrosetta library for naming (I ran into problems when the random number generator chose the same number for the next run and my script stopped working)

Note: My script is not perfect because I am new at writing code.  I just took help from scripts and then wrote pieces myself.


Thank you for your time and help!!!

Loop_compiled_script_7mer.txt5.93 KB
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Tue, 2019-10-08 12:50