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3D Structure Prediction

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3D Structure Prediction


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.



Sat, 2010-04-17 02:47

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

Mon, 2010-04-19 07:15