Dear rosetta users,
This is my first time using ab initio modelling in order to obtain a protein's structure (though i have some experience on comparative/homology modelling).
I'm trying to obtain the structure of 2 proteins of 89 (COR15A) and 90 (COR15B) residues respectively. Sadly i can't use the homology-modelling methodology because i don't have a proper template to use it.
Anyway, i have already built 100 structures of one of my protein (COR15B) by using the following command:
../../Downloads/rosetta_2014.20.56838_bundle/main/source/bin/AbinitioRelax.linuxgccrelease -database ../../Downloads/rosetta_2014.20.56838_bundle/main/database -in:file:fasta ./COR15B.fasta -in:file:frag3 ./aat000_03_05.200_v1_3 -in:file:frag9 ./aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -constant_seed -jran 5 -abinitio::rsd_wt_loop 0.5 -use_filters true -psipred_ss2 ./t000_.psipred_ss2 -kill_hairpins ./t000_.psipred_ss2 -out:file:silent COR15B_silent-5.out -nstruct 10 > COR15B-5.log &
I launched it 10 times changing the jran number in order to get the 100 structures, but my problem is that i'm getting really different structures, so basically i don't know which one i should use.
By using the command:
../../Downloads/rosetta_2014.20.56838_bundle/main/source/bin/cluster.linuxgccrelease -database ../../Downloads/rosetta_2014.20.56838_bundle/main/database/ -cluster:radius 3 -in:file:silent COR15B_silent-3.out -out:output -in:file:fullatom
i got 10 different clusters for the 10 initial structures, so each one of them are totally different from the other ones, right?
As i said you before, this is my first time using rosetta, so probably i'm making several things wrongs.
I was looking into the webpage for an specific workflow to use, but i couldn't find :/
So hopefully someone here could guide me on this task. (and also to how to use rosetta in a proper way )
Have a nice day,
Carlos Navarro Retamal