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Silent Files

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Silent Files

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.


Tue, 2009-12-22 09:22

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?

Tue, 2009-12-22 11:15

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?

Tue, 2009-12-22 13:11

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).

Wed, 2009-12-23 13:34