So I've run abinitiorelax for a protein and I now have a large number of good structures that I have extracted to *.pdb files. I have run this cluster command on them as well...
cluster.linuxgccrelease -database /opt/rosetta-3.2.1/rosetta_database/ -in:file:s *.pdb -in:file:fullatom -cluster:radius -1
Is this a good way to cluster or is there a better way to do this?
I'm also not sure what the best protocol is for finding the best structure. Could someone help me out with this, either just pointing me to the most recent best papers or by giving me a quick run down of a procedure would be great? I'm pretty new to all this and having a hard time figuring things out based on mainly just the manual for rosetta. Thanks for any help.