Silent Files

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    • December 22, 2009 at 5:22 pm #395
      Anonymous

        Is there a way to get RosettaDock to output only silentfiles, rather than the pdb files for all the poses? I know it is possible with RosettaLigand, but it doesn’t seem to work for RosettaDock.

        Thanks,
        Christy

      • December 22, 2009 at 7:15 pm #4283
        Anonymous

          I poked around in the code – it looks like the out::file::silent flag should work here to get silent output. Does it not?

          You mention “only” silent files – are you getting PDBs and silent files simultaneously?

        • December 22, 2009 at 9:11 pm #4284
          Anonymous

            Yes, that does work, thanks. However, when I try to output a PDB file using the extract script, it outputs everything as one chain. Is the extract script meant for the protein docking mode?

          • December 23, 2009 at 9:34 pm #4285
            Anonymous

              I’d guess not, if it’s giving you trouble. I haven’t used it. Are there other scripts in that folder to try? (I don’t have a copy of the user release handy.)

              I assume you’re trying to extract silent files to PDB; is this using the extract_pdbs executeable? You may be able to modify it or its options? Also, what type of silent file are you outputting from docking? You may have better luck with a binary silent file than whatever the default is (they store more information).

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