ab-initio and ab-relax protocols

Runing ab-initio

Input flags to run ab-initio protocol

-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5
-abinitio::rg_reweight 0.5
-abinitio::use_filters false
-abinitio::relax false
-silent_gz

-nstruct 1000
-increase_cycles 1

-frag3 1pqxA-multiR.3w.200.3mers
-frag9 1pqxA-multiR.3w.200.9mers

-in::file::native  1pqxA.pdb
-in::file::s       1pqxA.pdb

-out:file:silent 1pqxA-abinitio.out
-out:sf 1pqxA-abinitio.fsc

Running ab-relax

Just change -abinitio::relax false to -abinitio::relax true in the flag-file above

Using backbone NOE in centroid modeling

Add the two lines to the flag-file

-score::sspair_promoted ../1pqx.NOE
-score::sspair_promotion_factor 1.5