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question about scoring silent output files and their contents

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question about scoring silent output files and their contents

After clustering I created silent files for every cluster with the contents being the info from every structure in that cluster. I then went to score these silent files and output another silent file with the score results (one silent file for every cluster with the score values in it). My problem is that the silent file produced from running the score function contains not only the scores but also the info from the .pdbs for each structure. I would like this file to have only the score values for the structures in each cluster. Is there an easy way to accomplish this?

Here is the command I used to score the structures for each cluster.

score_jd2.linuxgccrelease -database /opt/rosetta-3.2.1/rosetta_database/ -in:file:silent c.1.silent -in:file:fullatom -out:file:silent c.1.score.silent

Thanks for any help.

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Wed, 2011-07-27 16:28

I'm not entirely clear on what the problem is, but I'm wondering if it's better addressed by grep than Rosetta? If the data are in your file already, is it easier to just strip them out of the file than regenerate it...?

Tue, 2011-08-02 13:14

I agree with Steven that greping for "SCORE:" lines is probably the better/faster way to do it, given you already have a scorefile.

For future reference, though, try omitting the "-out:file:silent" flag and use "-out:file:score_only -out:file:scorefile c.1.score" -- This should invoke the ScoreOnlyJobOutputter rather than the SilentFileJobOutputter (caveat: untested).

Tue, 2011-08-02 15:12