Unable to understand fragment picking tutorial points.

Dear Friends,

I am performing abinitio structure prediciton of a 382 long protein sequence by following the tutorial:

https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction

In this tutorial, there is a “fragment picking” tutorial:: https://www.rosettacommons.org/demos/latest/public/fragment_picking/README

Could you please help me understand the below bullet points of the tutorial? I am unabvle to link these below points with what I am supposed to do. Uptil psipred I  understand and have got .ss2 file. I have difficulty in uderstanding:

a) “put this vall in the flag”; where to get the vall from?

b) and, what does “flags” mean here? I think there is something missing in between in the tutorial. 

c) how to get a vall file like mentioned here: filtered.vall.dat.2006-05-05.gz?

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”

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• 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.

Thank you for your time!