3D Structure Prediction

Member Site Forums Rosetta 3 Rosetta 3 – General 3D Structure Prediction

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    • #584

        Hi ALL,

        I am quite new to ROSETTA and am trying to use ROSETTA3.1
        I want to predict a 3D structure of a protein having its sequence. However I find that the application “abinitio” asks for a “native PDB” in its flag (-in:file:native):

        -database Path to Rosetta databases. [PathVector]
        -abinitio:relax Do a relax after abinitio = abrelax, default=false.
        -in:file:native Native PDB filename. [File]
        -in:file:frag3 Fragments file with residue length of 3 [String]
        -in:file:frag9 Fragments file with residue length of 9 [String]
        -out:nstruct Number of times to process each input PDB. [Integer]
        -out:file:silent Use silent file output, use filename after this flag, default=default.out [String]
        -out:pdb Use PDB file output, default=false [Boolean]
        -out:path Path where PDB output files will be written to, default ‘.’

        How will I give a native PDB before predicting one? Or do I need to use some other executable instead of “AbinitioRelax.linuxgccrelease” to predict a 3D model. Any suggestion is welcome.



      • #4432

          The native is used for RMSD comparison (in the benchmarking prediction context, or for homology modeling). I think it should run ok without it…

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