I don't know if this is the appropriate place to ask this type of question but I have been reading this paper which describes the FastFloppyTail and Abinitio programs:
https://www.biorxiv.org/content/10.1101/2020.01.30.925636v1.full#F5
I am currently trying to generate 500 structures for an IDP called non-phosphorylated 4E-BP2 using the FastFloppyTail method. I used PsiPred DISOPRED3 to generate the secondary structure and disordered prediction files. I then used the Diso_SS2_Reweight_Opt_FFT.py script to reweight the secondary structure prediction based off of the disordered prediction file. I then submit my reweighted secondary structure prediction file and protein sequence into the Robetta web server to generate the 3mer fragments. I then utilize FastFloppyTail to generate the protein structures using the 3mer fragments (I am not using the -diso option, but maybe I should?).
My questions are: Do I have to use AbInitio before I use FastFloppyTail as indicated by Figure 1 in the above paper that I linked or is that only for mostly ordered proteins that have IDRs rather than an IDP? Could I supply the -t _frag option with 9mer fragments instead of 3mer fragments?
Thanks,
Thomas
You may need to ask the authors, I'm asking around to confirm but they do not appear to be part of RosettaCommons directly. May I suggest opening an Issue in their Github? (https://github.com/jferrie3/AbInitioVO-and-FastFloppyTail/issues)
I have emailed the authors and if they do not respond I will open an issue in their Github. Thanks for the quick reply!