AMBER Archive (2008)

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

From: Jianyin Shao (
Date: Wed May 28 2008 - 23:07:18 CDT

On 5/28/08, Dong Xu <> wrote:
> Hi Jianyin,
> Does the cluster command already include rms fit? I tried on a
> trajectory without doing rms fit at first and the output
> representative structure look they are rms aligned on the atom select
> mask used in the cluster command.

 The clustering does not do an explicit rms fit. However, it makes sense to
do rms fit before calculating the centroid (average structure). So all
structures will align to the representative structure of the most populous
cluster before outputing. For those agglomerative algorithms and k-mean
algorithm, rms fit is not required. Other algorithms will need an explicit
rms fit command before clustering.

If this is the case, how to disable rms fit in cluster command? Do we
> have something similar to "nofit" in rms command?

 As I just said, rms fitting is required for calculating meaningful
centroids. Is there a specific reason you don't want rms fitting?



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