I recently downloaded the I-Tasser standalone package (version 3) and would like to use it to predict the 3D structure of a protein.
However, I am unsure how to go about doing this. I read the Readme file but the instructions are unclear considering I don't have a strong background in with this software. I don't know what is meant by
a) Main script for running I-TASSER is $pkgdir/I-TASSERmod/runI-TASSER.pl.
Run it directly without arguments will output the help information.
b) The following arguments must be set mandatorily. One example is:
"$pkgdir/I-TASSERmod/runI-TASSER.pl -pkgdir /home/yourname/I-TASSER3.0 -libdir /home/yourname/ITLIB -seqname 1a2bA -datadir /home/yourname/1a2bA -usrname yourname -java_home /usr/java/latest"
Is this supposed to be pasted into cmd? Or do I simply need my fasta sequence and I can paste this into the program? Any help would be appreciated.