Hi Sundar,
It looks to me like a simple occupancy table in text that shows which
cluster each frames belongs to. Unfortunately I have never tried post
processing this format of file so unless someone has a script they have
written that they can send you you'll probably have to write something to
parse the file yourself. This shouldn't be too difficult to do. A perl
script that parses the text output into something that is readable by
xmgrace should be fairly simple to do. You ultimately just need a column for
time and a number representing the cluster.
Alternatively you could simply modify the ptraj code to output the data in
the format you want. It has to have the data structures to produce the text
file so just add some additional write statements to build a file containing
time vs cluster id.
Good luck,
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of S.Sundar Raman
> Sent: Wednesday, March 11, 2009 7:58 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Seeking for suggestion related to plot the cluster
> out file
>
> Dear Ross,
> Thanks for your reply.
> I find significant difference between the cluster.txt which i attached
> with
> this mail with the one they showed in the tutorial.
> In the tutorial ( which is version amber9 with *MMTSB Toolset) * the
> distance from the centroid is given and i did not find such information in
> my file ( amber tools 1.2 version). On the other hand in my file with
> respect to time it give which group of cluster is exist.
>
> therefore I am seeking for help to plot from this file
> with regards
> sundar
>
> On Wed, Mar 11, 2009 at 3:33 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi Sundar,
> >
> > I suggest taking a look at the clustering section (section 6) in the
> > following tutorial: http://ambermd.org/tutorials/basic/tutorial3/
> >
> > This will show you how you can plot the cluster id's against time etc so
> > that you can see when each cluster occurs etc.
> >
> > Good luck,
> > Ross
> >
> > > -----Original Message-----
> > > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > > Behalf Of S.Sundar Raman
> > > Sent: Wednesday, March 11, 2009 5:44 AM
> > > To: AMBER Mailing List
> > > Subject: [AMBER] Seeking for suggestion related to plot the cluster
> out
> > > file
> > >
> > > Dear amber users,
> > > I am trying analyse the output of clustering. I used the following
> > > commands
> > > in the ptraj to do clustering.
> > >
> > > trajin /data/mcm/subramsn/simulation/prot/prot_new1.dyn5.nc
> > > strip :WAT
> > > rms first mass :1-367 name rmsd
> > > cluster out prot_cluster representative pdb average pdb means clusters
> 5
> > > rms.CA
> > >
> > > I got the following output files.
> > > five cluster average structure files
> > > five cluster representative files
> > > five cluster trajectory files
> > > one cluster.txt file
> > > As i read from the research article I can understand the centroid
> values
> > > of
> > > each cluster.
> > > I would like to draw a plot from cluster.txt file as how each cluster
> is
> > > distributed in the trajectory and how one cluster is different from
> the
> > > other.
> > > I am seeking for a help in this regard. Eagerly waiting for reply.
> > >
> > > with regards
> > > sundar
> > > --
> > > S.Sundar Raman
> > > CSIR-SRF
> > > Chemical Laboratory
> > > Central Leather Research Institute
> > > Adyar, Chennai, India- 600 020
> > > &
> > > DAAD Research Scholar
> > > EML
> > > Schloss-Wolfsbrunnenweg 33
> > > D-69118 Heidelberg
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> S.Sundar Raman
> CSIR-SRF
> Chemical Laboratory
> Central Leather Research Institute
> Adyar, Chennai, India- 600 020
> &
> DAAD Research Scholar
> EML-Research,Villa Bosch,
> Schloss-Wolfsbrunnenweg 33
> D-69118 Heidelberg
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Received on Fri Mar 13 2009 - 01:11:15 PDT
