working with silent output – mergin, clustering and extracting

[Sally Ride]

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?

[Anonymous]

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?

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