AMBER Archive (2008)

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

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Tue Jul 29 2008 - 02:40:04 CDT

Hi Jianyin and Tom,

I was wondering if there's tutorial about how to plot the dendrogram
from ptraj clustering outputs. I see you used
http://www.bioinformatics.nl/tools/plottree.html in the ptraj
clustering paper. But I still can't figure out how to use that web
site and obtain PHYLIP format from ptraj outputs. Could you shed some
light on this topic?

Thanks a lot in advance,

-DX

On Tue, Jul 8, 2008 at 9:45 PM, Jianyin Shao <jyshao2004_at_gmail.com> wrote:
>
>
> On 7/8/08, Dong Xu <d1xu_at_ucsd.edu> wrote:
>>
>>
>>>
>>> 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.
>>
>> Thanks for the info. Would mind telling me what integer is commonly used?
>> I'm curious.
>
>
> You can try 6 or 7.
>>>
>>> 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.
>>
>> Do you Readmerge will not overwrite PairwiseDistance file if it's ready
>> present in the current folder?
>
>
> If a correct PairwiseDistances file exists in the current directory, the
> Readmerge will read it. If not, Readmerge will calculate the distance on the
> fly, but it will not write or overwrite a PairwiseDistances 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.
>>
>> Ok, just FYI. I ran it on a new machine and it turned out using more than
>> 10.5GB ram. I have another larger system that ended up using 18GB ram with
>> this perl script.
>>
>> Thanks,
>>
>> Dong Xu
>>
>>>
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