Hi,
Yes, these are the AC lines.
So you can see that the program did clustering at 8.209858 rmsd threshold to get the top closter of size 15. AC line can show you what would happen with lower threshold but you need to specify lower bound for the minimum size of the top cluster (15 members at present).
Please to clustering with the following options:
5,5,15,20 3,4
however anyway you need to generate more decoys. And you should really open the files with names such as ” cluster00.015.pdb” in any molecular viewer which can read CA traces (pymol, ramol) and see whether structures from a single cluster have the same fold at the given rmsd threshold.
> is this the AC lines?
>
> COMMAND: ../../C/cluster_info_silent.out bbphad.out _ cluster1/tmp 5,15,45,75 3,4
> AC: target 15 threshold 8.21 clusters 69 coverage 466
> AC: target 16 threshold 8.21 clusters 69 coverage 466
> AC: target 17 threshold 8.21 clusters 69 coverage 466
> AC: target 18 threshold 8.37 clusters 88 coverage 616
> AC: target 19 threshold 8.37 clusters 88 coverage 616
> AC: target 20 threshold 8.37 clusters 88 coverage 616
> AC: target 21 threshold 8.39 clusters 89 coverage 628
> AC: target 22 threshold 8.40 clusters 91 coverage 639
> AC: target 23 threshold 8.40 clusters 91 coverage 639
> AC: target 24 threshold 8.40 clusters 91 coverage 639
> AC: target 25 threshold 8.55 clusters 115 coverage 819
> AC: target 27 threshold 8.55 clusters 115 coverage 819
> AC: target 29 threshold 8.61 clusters 120 coverage 870
> AC: target 31 threshold 8.64 clusters 126 coverage 916
> AC: target 33 threshold 8.64 clusters 126 coverage 916
> AC: target 35 threshold 8.65 clusters 128 coverage 931
> AC: target 38 threshold 8.80 clusters 156 coverage 1192
> AC: target 41 threshold 8.87 clusters 165 coverage 1295
> AC: target 44 threshold 8.87 clusters 166 coverage 1305
> AC: target 47 threshold 8.88 clusters 167 coverage 1311
> AC: target 51 threshold 8.97 clusters 181 coverage 1453
> AC: target 55 threshold 8.99 clusters 185 coverage 1493
> AC: target 60 threshold 9.10 clusters 201 coverage 1700
> AC: target 65 threshold 9.16 clusters 220 coverage 1867
> AC: target 71 threshold 9.22 clusters 227 coverage 1994
> TARGET: 15 THRESHOLD: 8.209858
>
> what’s ur comment?
>
>
> > > how do u know my decoy above 8A.
> >
> > On the X axis of your clustering tree you have got rmsd values… You should be able to find the exact rmsd cutoff used for clustering in the *.info file you should have got in the clustering directory. It should be a line like:
> >
> > TARGET: 100 THRESHOLD: 1.271307
> >
> > just after the AC lines.
> >
> > > i am generate 9999 decoy
> >
> > For such a long protein it might be much too few. Especially if you get poor clustering.
> >
> > > run cluster_info_silent.out with 5,15,45,75 3,4
> >
> > With such options the program did not find any cluster with the size above 15 when using rmsd threshold between 3 and 4 A. So it increased the rmsd threshold until it got the top cluster of size 15.
> >
> > Please post the AC lines from your *.info file so I could advice you how you should modify the clustering options.
> >
> > And if you have computational power generate another 20000 decoys 
You can try different options/protocols or try to fold a homolog.
> >
> >
> >
> >