Extracting a part of a silent file as another silent file

[Anonymous]

Dear all,

I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.

First, I extracted the top 10% by sorting the I_sc with:

sort -n -k2 example_score_file.sc | head -n 1000 | awk ‘{print $2 “t” $25 “t” $NF}’ > score_I-sc_tag.dat

Then I used extract_pdbs.linuxgccrelease to extracts all the solutions with the tags, as pdb files.

Now, how can I extract the top 10% solutions from the parent silent file, as a silent file, whitout extracting the single pdb files?

 

Thanks in advance,

-Yasser

 

[Anonymous]

Hello Yasser!

in your scorefile, the last column should be ‘description’. This column holds the tags of each structure.

If you collect the tags for all the structures you want to extract, you can use the following script:

Rosetta/tools/analysis/extract_pdbs_from_pdbsilent_by_tags.py

usage: extract_pdbs_from_pdbsilent_by_tags.py silent_file tagsfile 

tagsfile is endline-delimited list of tags to extract;

silent_file is a PDB-silent-file

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