Explanations to membrane_abinitio options

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    • #457

        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:


        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!

      • #4342

          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…

        • #4343

            Hi Justin,

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

            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.

            • #4347

                Got it!

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

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