problem with fixed_membrane option of membrane abinitio

[Anonymous]

Hi to all

I want the models of membrane abinitio in the same membrane center vector and membrane normal vector, so I used the option -membrane:fixed_membrane to get the center at [0,0,0] and membrane normal in the z-axis

I use this arguments to run “membraneabinitio”::

-abinitio:membrane
-in:file:fasta ../rosetta_inputs/cterm.fasta
-in:file:frag3 ../rosetta_inputs/aat000_03_05.200_v1_3
-in:file:frag9 ../rosetta_inputs/aat000_09_05.200_v1_3
-in:file:spanfile ../rosetta_inputs/cterm.span
-in:file:lipofile ../rosetta_inputs/cterm.lips4
-membrane:fixed_membrane
-membrane:no_interpolate_Mpair
-membrane:Menv_penalties
-membrane:normal_start_angle 0
-membrane:normal_delta_angle 5
-membrane:normal_max_angle 5
-score:find_neighbors_3dgrid
-increase_cycles 0.05
-out:nstruct 3
-out:file:silent cterm_silent.out
-out:file:silent_struct_type binary
-run:no_prof_info_in_silentout
-mute core.io.database
-mute core.scoring.MembranePotential
-database ${ROSETTA}/rosetta_database

and later I get the pdbs from the binary output with “score” using this arguments:

-in:file:fasta ../rosetta_inputs/cterm.fasta
-in:file:centroid_input
-in:file:silent cterm_silent.out
-in:file:silent_struct_type binary
-in:file:spanfile ../rosetta_inputs/cterm.span
-in:file:lipofile ../rosetta_inputs/cterm.lips4
-membrane:no_interpolate_Mpair
-membrane:Menv_penalties
-score:find_neighbors_3dgrid
-score:weights score_membrane.wts
-out:nstruct 1
-database ${ROSETTA}/rosetta_database
-out:output
-nstruct 1

But the output log give me this kind of results::

…
core.scoring.MembranePotential: MembraneCenter 17.593 5.919 -5.684
core.scoring.MembranePotential: MembraneNormal -0.440 -0.400 0.804
core.scoring.MembranePotential: ATOM 9999 X MEM A 999 17.593 5.919 -5.684
core.scoring.MembranePotential: ATOM 9999 Y MEM A 999 10.986 -0.077 6.374
core.scoring.MembranePotential: ATOM 9999 Z MEM A 999 24.199 11.915 -17.74

What I did wrong to have this??

Thx in advance
Regards

[Anonymous]

A) I don’t know enough (really I don’t know anything) about membrane abinitio – why does that output concern you? It looks like some sort of membrane virtual atom.

Are the PDBs okay or not? If you are going to extract _all_ the PDBs, there’s no reason to do the separate score app step at all – just remove the -out:file:silent flags from the first list of arguments and it ought to output PDBs instead.

[Anonymous]

A) I put unnecessary information of the stdout
but the important are these lines

core.scoring.MembranePotential: MembraneCenter 17.593 5.919 -5.684
core.scoring.MembranePotential: MembraneNormal -0.440 -0.400 0.804

With the argument fixed_membrane the membrane center should be 0 0 0 and not 17.593 5.919 -5.684

I dont have problem with the PDBs output

[Anonymous]

I can’t tell if it’s a problem or not; I’ve asked the author for advice.

[Author]

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