Reply To: Explanations to membrane_abinitio options

[Anonymous]

Hi Justin,

-membrane:no_interpolate_Mpair
This flag will switch off the interpolation between the two layers for the pair-term to mimic the old code

-membrane:Menv_penalties
This flag will switch on the following penalties:
* no non-helical secondary structure fragments in predicted transmembrane helical regions in the hydrophobic layer of the membrane.
* no N- and C- termini residues of predicted transmembrane helical regions in the hydrophobic layer of the membrane.
* no transmembrane helices with orientation >45 degrees relative to the membrane normal vector.

Based on our benchmarking of the rosetta-membrane code, these options improved performance of the ab initio protocol. I’ll add description of these options to the next Rosetta release.

We don’t use -smooth_move_frac flag – I’ll check with one of the original developers of the code to see if we can remove it as well as tmp and debug options.