Explanations to membrane_abinitio options

[Anonymous]

Dear all,

I am doing ab initio prediction of a membrane protein. The manual for rosetta3.1 version gives an example.
Unfortunately, I can not find out what these options mean:

-membrane:no_interpolate_Mpair
-membrane:Menv_penalties

I get some information from the “help”, but no description is given.

smooth_move_frac | 0.5 | R| No description
no_interpolate_Mpair | false | B| No description
Menv_penalties | false | B| No description
tmp_real1 | 1 | R| No description
tmp_real2 | 1 | R| No description
tmp_real3 | 1 | R| No description
tmp_int1 | 1 | I| No description
tmp_int2 | 1 | I| No description
tmp_int3 | 1 | I| No description
tmp_bool1 | false | B| No description
tmp_bool2 | false | B| No description
tmp_bool3 | false | B| No description
debug | false | B| No description
Any one can help me?
Thank you a lot!

[Anonymous]

The tmp and debug options do nothing of interest, as far as I can tell.

The first three you mention are called in the code but I don’t know what they do. I’ll see if I can contact the original authors…

[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.

[Anonymous]

Got it!

Thank you a lot!!!!!(:smile:)

[Author]

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