AMBER Archive (2008)

Subject: Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9

From: Jianyin Shao (
Date: Tue May 27 2008 - 14:29:43 CDT

On 5/27/08, Dong Xu <> wrote:
> If I want to fix the seed structure that I provide for decoy, I will
> have to specify "iteration 1", correct?

If you specify "iteration 1", the clustering will stop after assigning each
frame to the closest seed. If no iteration value is specified, the K-means
refinement will kick in with the default iteration value of 50.

So I tried it and compared my input seeds (averagelinkage cluster
> representatives) and decoy output representatives. They look
> different. I remember the paper mentioned that the representative are
> not the centroid, but a structure close to the centroid instead. Is
> that the reason why representatives deviate from the seeds even if I
> use "iteration 1"? Centroid is not necessarily an actual frame from
> the trajectory, but a representative is, correct?

The centroid is the average structure of the a cluster, it is not a real
structure and may not look like a real one. The representative structure is
a real structure from the trajectory that is closest to the centroid of its
cluster. If the averagelinkage clustering result is different from the decoy
result, it is possible that their representatives are not same.

Good luck,


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