- This topic has 3 replies, 3 voices, and was last updated 13 years, 10 months ago by Anonymous.
February 10, 2010 at 9:14 am #457Anonymous
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!
February 10, 2010 at 3:38 pm #4342Anonymous
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…
February 10, 2010 at 5:49 pm #4343Anonymous
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.
February 11, 2010 at 7:43 am #4347Anonymous
Thank you a lot!!!!!(:smile:)
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