AMBER Archive (2008)

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

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Mon Jul 07 2008 - 17:41:03 CDT

Hi, Dong,

The syntax for verbose is "verbose" followed by an integer. The purpose is
to let the developer check some internal information during the clustering.
Using "verbose" option may generate excessive output and cause confusion,
thus not advised.

Readmerge does not require the file PairwiseDistances to be present. It
will calculate the (rms-fitted) distances between frames, but will not try
to rewrite a new PairwiseDistance file.

I don't know how to estimate the memory usage in Perl. The memory management
in Perl is mostly automatic, that is why I feel it is easy to write a
script. Maybe someone else can help me with that. I will let you know when
the silhouette function is fully incorporated in the ptraj.

Hope that helps.

Jianyin

On Fri, Jul 4, 2008 at 1:21 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:

> Hi Jianyin,
>
> The silhouette.pl script froze my computer with 4GB ram when I ran it on a
> 570MB PairwiseDistances and 12140 frames in ClusterMerging.txt. I wonder if
> there's a way to estimate the memory usage and run time based on the input
> filesize? Do you have any silhouette programs that are binaries compiled in
> C or Fortran?
>
> Thanks,
>
> Dong
>
>
> On Thu, Jul 3, 2008 at 11:33 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:
>
>> Also, when you use "Readmerge" to read ClusterMerging.txt generated by
>> averagelinkage, does PairwiseDistances file have to be present? If not, will
>> Readmerge re-calculate PairwiseDistances?
>>
>> Thanks,
>>
>> -DX
>>
>>
>> On Thu, Jul 3, 2008 at 11:28 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:
>>
>>> 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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