I am performing abinitio structure prediciton of a 382 long protein sequence by following the tutorial:
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:
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:
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!
frags.200.3mers: for use with
frags.200.9mers: for use with
- fsc files for fragment information.
Thank you for your time!