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