I would like to run rosetta and analyze its results as following:
1) Generate decoys in silent format with multiple rosetta runs (that is I have several *.out files)
2) Cluster all decoys together
3) Extract structures corresponding to the decoys from best clusters in pdb format
Sounds easy but:
* decoys in *.out files from different rosetta runs have the same numbers (in each silent file they start from S_1) so I cannot simply concatenate the files
* I know rosetta -extract but I would need some simple custom script to get decoys corresponding to the best clusters.
* I would like to rebuild full atom pdb files
Has anybody good protocol for that?
Maybe you can change your native pdb to be different name as 1xxxa, 1xxxb, 1xxxc to avoid lose data during extracting silent files.
> I would like to run rosetta and analyze its results as following:
>
> 1) Generate decoys in silent format with multiple rosetta runs (that is I have several *.out files)
>
> 2) Cluster all decoys together
>
> 3) Extract structures corresponding to the decoys from best clusters in pdb format
>
> Sounds easy but:
>
> * decoys in *.out files from different rosetta runs have the same numbers (in each silent file they start from S_1) so I cannot simply concatenate the files
>
> * I know rosetta -extract but I would need some simple custom script to get decoys corresponding to the best clusters.
>
> * I would like to rebuild full atom pdb files
>
> Has anybody good protocol for that?