AMBER Archive (2008)

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

From: Jianyin Shao (
Date: Fri May 30 2008 - 12:11:24 CDT

I understand that "X" labels the correspondent frames to the cluster
> members. I wrote a python script to translate "X" to frame number. But
> what I wanted to know was how to obtain or extract the frame numbers
> for the cluster representatives in "" files.

One "dumb" trick you may try is to use the representative structure as
reference and run rms fitting for the entire trajectory. The one with rmsd
of 0 should be the representative frame.

> Since ptraj already has "rms" command, rms fitting in clustering seems
> a bit redundant if "rms" command is explicitly required prior to
> running "cluster" command.

The rms command will fit to a specific structure. In clustering, the
structures in the trajectory will be aligned to different representative
structures of clusters to obtain reasonable centroids.

Good luck,


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