how do u know my decoy above 8A.
i am generate 9999 decoy
run cluster_info_silent.out with 5,15,45,75 3,4
what ur comment
> Well, it does not look very good… Look at the rmsd values: they are pretty high (above 8A) and clusters are in the same time quite small. In the prefix.info file you should be able to find the exact rmsd cutoff which was used for the clustering. I would check the superposition of the decoys in five top clusters to see what 8A actually means for your protein. You should have the CA superpositions in files with names such as cluster00.015.pdb. If the decoys are virtually dissimilar you need to go down with the rmsd threshold (by manipulating cluster_info_silent.out options). But then of course you would get smaller clusters (and I would not be sure whether clusters with less then 10 members are meaningful at all…).
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> Maybe indeed you need to generate more decoys (how many you got so far?) or run rosetta with different options. Maybe it is possible to split your protein into two domains?
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> Frankly, I have never succeeded folding with rosetta a protein as long as yours. But certainly I do not use so big computational resources as some rosetta power users 
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> > can u please go to this blog:
> > http://icbbio.blogspot.com/
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> > what is your comment about this clustering tree
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> > is there any good decoy to start protein modelling