AMBER Archive (2008)

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

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Fri Jul 04 2008 - 01:28:44 CDT

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.

Thanks,

-DX

On Fri, May 30, 2008 at 10:11 AM, Jianyin Shao <jyshao2004_at_gmail.com> 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 "filename.rep.ci" 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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