Selecting Top Scoring Decoys

Member Site Forums Rosetta 3 Rosetta 3 – General Selecting Top Scoring Decoys

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    • #1060


        I have a silent file of 20,000 decoys and I want to extract/separate low energy decoys out to a separate silent file for all atom relax. Is there any possibility of doing it. I tried cluster.linuxgccrelease with -cluster:output_score_filter and it doesn’t seem to work! Is there any workaround or possibilities of any script!

      • #6156

          I think the score application takes in:file:tags, which is a list of the tags. You can filter which structures you want by sorting the scorefile, then put the structure names in a file and pass that to tags; then try telling score mode to use silent input and silent output. (I have no idea if this is the right solution or if it will work, but it’s worth a shot).

        • #6157

            It looks like the relax application has been jd2 for over a year now, so the standard flags for controlling silent file input with jd2 (such as -in:file:tags) should also work with the relax application directly (at least for 3.2 and 3.3) – no need to split them off into a separate file first.

            One clarification, though. From my reading of the code, -in:file:tags takes the list of tags themselves, rather than taking a filename of a file containing the list of tags. If you’re using a bash-like shell to run the job, though, it’s easy enough to work around that. Just do something like “-in:file:tags `cat listoftags.txt`”, where it’s backticks around the “cat” command. (The backticks tell bash to run the command and place the output on the command line in its place.)

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