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. (firstname.lastname@example.org) 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.