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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:
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> 1) Generate decoys in silent format with multiple rosetta runs (that is I have several *.out files)
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> 2) Cluster all decoys together
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> 3) Extract structures corresponding to the decoys from best clusters in pdb format
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> Sounds easy but:
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> * 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
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> * I know rosetta -extract but I would need some simple custom script to get decoys corresponding to the best clusters.
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> * I would like to rebuild full atom pdb files
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> Has anybody good protocol for that?