AMBER Archive (2009)

Subject: Re: [AMBER] Seeking for suggestion related to plot the cluster out file

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Wed Mar 11 2009 - 11:07:25 CDT

Dear Ross,

thanks for your suggestion.
with regards
sundar
On Wed, Mar 11, 2009 at 4:55 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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_at_ambermd.org [mailto:amber-bounces_at_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_at_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_at_ambermd.org [mailto:amber-bounces_at_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_at_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_at_ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_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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