AMBER Archive (2008)

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

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Sat Aug 02 2008 - 21:23:53 CDT

Hi, Dong,

The ClusteringSplitting.txt is generated by hierarchical algorithm,
just like the ClusteringMerging.txt to the linkage/edge/complete/..
algorithms.

Best,

Jianyin

On 8/2/08, Dong Xu <d1xu_at_ucsd.edu> wrote:
>
> Hi Jianyin,
>
> A quick questions. I know ClusteringMerging.txt is the output of ptraj
> clustering. How do you get ClusteringSplitting.txt file though?
>
> Thanks,
>
> Dong
>
> On Fri, Aug 1, 2008 at 1:21 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:
> > Hi Jianyin,
> >
> > Thanks for the new script. Kevin and I will try it out and let you if
> > it works out.
> >
> > Best,
> >
> > Dong
> >
> > On Fri, Aug 1, 2008 at 12:43 PM, Jianyin Shao <jyshao2004_at_gmail.com>
> wrote:
> >> Hi, Dong and Kevin,
> >>
> >> I am sorry that I sent you the wrong script. Please discard the
> Newick.pl
> >> script. Instead use the Newick-step.pl I attached this time.
> >> The script requires a ClusteringMerging.txt or ClusteringSplitting.txt
> file
> >> and total number of frames in the trajectory, also you can provide a
> number
> >> n to show the last n steps of merging. The previous Newick.pl generates
> all
> >> steps, which the plottree cannot handle.
> >>
> >> Best,
> >>
> >> Jianyin
> >>
> >>
> >>
> >>
> >>
> >> On Fri, Aug 1, 2008 at 3:39 AM, Kevin Wu <kjwu_at_ucsd.edu> wrote:
> >>>
> >>> Hi Jianyin,
> >>>
> >>> Recently Dong Xu contacted you about plotting denograms from ptraj
> >>> clustering outputs, he forwarded it for me to figure it out. You told
> him to
> >>> use the "Newick" perl script to get it into the PHYLIP format. I looked
> at
> >>> "Newick.pl -h" and I tried to run the command:
> >>>
> >>> ./Newick.pl -in ClusterMerging.txt -out Newick.txt -mode merge -count
> 1572
> >>>
> >>> There was no error message outputted and Newick.txt didn't look out of
> the
> >>> ordinary. The output Newick.txt is attached. However, when I submit to
> tree
> >>> plot web service, "http://www.bioinformatics.nl/tools/plottree.html ",
> in
> >>> your ptraj clustering paper I get the error: "Premature end of script
> >>> headers: showtree". Am I doing something wrong?
> >>>
> >>> I searched for another plotting program called njplot to see if it was
> >>> just the server, and the program told me that its not a "correct tree".
> Let
> >>> me know what I'm doing wrong. Thanks for your time!
> >>>
> >>> Regards,
> >>> Kevin
> >>
> >>
> >>
> >> On Tue, Jul 29, 2008 at 1:40 AM, Dong Xu <d1xu_at_ucsd.edu> wrote:
> >>>
> >>> 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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