The scripts and input files that accompany this demo can be found in the demos/public directory of the Rosetta weekly releases.

KEYWORDS: DESIGN GENERAL

Demo last modified by Vikram K. Mulligan, Ph.D. (vmullig@uw.edu) during the 2016 Documentation eXtreme Rosetta Workshop (XRW).

This is a demo of a very simple design protocol run on a fixed backbone. If you have never run Rosetta before, then this is a good first demo to run, because it is very simple and has few options.

  • The demo can be run like this:

    <path_to_Rosetta_directory>/main/source/bin/fixbb.default.linuxgccrelease -in:file:s 1l2y.pdb >log.txt &

    The above should take on the order of ten seconds to run. During that time, you will be able to use the command prompt. The following files should be produced:

      1l2y_0001.pdb
  log.txt
  score.sc

  • Open the structure and the input structure in pymol to observe sequence changes from design.

  • Systematically list sequence changes in the form of a sequence profile:

    ls 1l2y_0001.pdb > list.txt  # this would typically be many designed structures all in a list
python $ROSETTA_TOOLS/protein_tools/scripts/SequenceProfile.py -l list.txt -t 1l2y.pdb

    In the above, the ROSETTA_TOOLS environment variable must be set to point to your Rosetta/tools directory. Alternatively, you may manually type the location of the Rosetta/tools directory.

  • To control which residues are allowed at each sequence position you would add a resfile (included in this demo) like so. (Note that we're also changing appending the suffix "_resout" to the output PDB files so as not to overwrite the files produced previously.):

      rosetta/rosetta_source/bin/fixbb.default.linuxgccrelease -in:file:s 1l2y.pdb -resfile resfile.txt -out:suffix _resout > log_resout.txt &

  • Open up the resfile.txt file to see its format. Briefly, NATRO leaves the natural rotamer (and amino acid). NATAA leaves the amino acid at a position but allows rotamer to change. ALLAA allows full design with any amino acid. PIKAA followed by a list of single-letter-code amino acids restricts design to just those amino acids. So, for example:

      1 A PIKAA NT

    indicates that residue 1 can be either N or T.