RASREC – finding lowest energy structure

[Anonymous]

Hi Rosetta community,

After finally getting the RASREC run to successfully generate full 6 stages, now I’m at the point where I want to score the pdbs to find the lowest energy structures which suppose to be the closest to the native structure. But in this website: https://www.rosettacommons.org/demos/latest/protocol_capture/rasrec_evolutionary_restraints/README

there’re no instructions on plotting, however, there’s a script for finding 30 structures with the lowest scoring value from the silent.out file.

The script is this:

extract_decoys decoys.out -score 30 > low_30.out

This generates 30 structures with the lowest energy value, which then I converted to pdbs. Now I’m wondering, can I use a similar script to produce one structure with the lowest energy? I used this script to generated one structure with the lowest energy value “extract_decoys low_30.out -score 1 > low_1.out”.

The structure I got seems legit, meaning that it seems to incoporate all the restraints I added to the run (Chemical Shifts, membrane restraints). Do you think it is suffeicnet to just leave it at that or am i missing something?

I would appriciate your advice.

Thanks!

[Anonymous]

I don’t have much experience with RASREC, but I talked with someone who should know, and he suggested you post to http://csrosetta.chemistry.ucsc.edu/forum on the CS-Rosetta website, to see if people there can help.

[Anonymous]

Thanks rmoretti! But the link to the forum you gave me doesn’t allow me to post anything. Last post in it is 9 months ago. 

RASREC has poor documentations and it’s not helpful at all having an inactive forum to top that! 

 

[Author]

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