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

KEYWORDS: STRUCTURE_PREDICTION UTILITIES

Do the best picker option for the starter demo:

./BestFragmentsProtocol/

Submit the following sequence (in the FASTA format) to psipred:

> 2JSV X
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE

After psipred finishes get the "download the machine learning scores results in plain text format" and give it a meaningful name, e.g. 2jsv.psipred.ss2. This should have a header with the string "VFORMAT"

  • Put this vall in the flags:

    $ <path-to-Rosetta>/main/database/sampling/filtered.vall.dat.2006-05-05.gz

    Update the flags with your correct database location

  • Run the picker like this:

$> $ROSETTA3/bin/fragment_picker.linuxgccrelease @BestFragmentsProtocol/flags -in::file::vall $ROSETTA3_DB/sampling/small.vall.gz

IMPORTANT The small.vall.gz used here for fragment picking is only used to speed up the demo. You have to change this to the vall database on your system!

Output:

  • frags.200.3mers: for use with -in:file:frag3
  • frags.200.9mers: for use with -in:file:frag9
  • fsc files for fragment information.

  • Now get the quality of these 3-mer fragments:

    $> $ROSETTA3/bin/r_frag_quality.linuxgccrelease -in:file:native BestFragmentsProtocol/input_files/2jsvX.pdb -f BestFragmentsProtocol/output_files/frags.200.3mers

    Output:

    • frag_qual.dat

    Use gnuplot to visualize the quality data:

      plot "frag_qual.dat" u 2:4 w p

    This command simply makes a scatter plot with column 2 on the x-axis and column 4 on the y-axis.

More detailed information in:
Rosetta Documentation

Tweak the fragment picker

There many ways to influence how fragments are being picked. Many options are described in the Rosetta Documentation.

The various subdirectories of this demo serve as repository for examples:

./NullFragments  
./fragment_picking_for_flexible_loop_design
./fragment_picking_torsion_class_score
./fragment_picking_with_quota
./fragment_picking_with_quota_and_restraints

You can test them:

$> $ROSETTA3/bin/fragment_picker.linuxgccrelease @NullFragments/flags -in::file::vall $ROSETTA3_DB/sampling/small.vall.gz
$ $ROSETTA3/bin/fragment_picker.linuxgccrelease @fragment_picking_for_flexible_loop_design/flags -in::file::vall $ROSETTA3_DB/sampling/small.vall.gz
$> $ROSETTA3/bin/fragment_picker.linuxgccrelease @fragment_picking_torsion_class_score/flags -in::file::vall $ROSETTA3_DB/sampling/small.vall.gz
$> $ROSETTA3/bin/fragment_picker.linuxgccrelease @fragment_picking_with_quota/flags -in::file::vall $ROSETTA3_DB/sampling/small.vall.gz
$> $ROSETTA3/bin/fragment_picker.linuxgccrelease @fragment_picking_with_quota_and_restraints/flags -in::file::vall $ROSETTA3_DB/sampling/small.vall.gz

The fragment files can be found in /output_files. There are example outputs already. The newly generated ones will contains ".200". So, you can check whether it worked.

IMPORTANT The small.vall.gz used here for fragment picking is only used to speed up the demo. You have to change this to the vall database on your system!