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

From: Dong Xu <>
Date: Thu, 3 Jul 2008 23:28:44 -0700

Hi Jianyin,

I see there's an option [verbose *verb*]. Could you tell me how to use. The
clustering manual didn't mention it at all.



On Fri, May 30, 2008 at 10:11 AM, Jianyin Shao <> wrote:
>> 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,
> Jianyin

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Received on Sun Jul 06 2008 - 06:07:41 PDT
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