# Re: [AMBER] Interpreting the distance covariance matrix

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Tue, 14 Jun 2011 21:09:15 -0400

Hi Mariano,

Yeah. Things are starting to make sense. But what I really want to find out
is that how each residue is coupled to eachother and NOT how that coupling
parameter changes with respect to eachother. So what I need is something in
the format of 22 by 22 which shows how one is coupled to the other. Do you
think the corresponding covariance matrix will hv that format? Coz this 231
by 231 does not seem to fulfill my purpose that much. Do you have any
suggestions?

Best regards

Sajeewa

On Tue, Jun 14, 2011 at 8:22 PM, Mariano Rech <mariano.rech.gmail.com>wrote:

> Hi Sergio and Sajeewa
>
> I do not really understand what should be the problem:
> if you have N variables and you want to look at how they vary the one
> respect to the other, you can build a covariance matrix N x N
>
> in your case Sajeewa you have 231 variables (the pairwise distances between
> CAs) hence you will have a covariance matrix 231 x 231
> ...
> Regards
>
>
> 2011/6/15 Sajeewa Pemasinghe <sajeewasp.gmail.com>
>
> > Thank you very much. I'll try to figure it out.
> >
> > On Tue, Jun 14, 2011 at 7:40 PM, Sergio R Aragon <aragons.sfsu.edu>
> wrote:
> >
> > > Hello Sajeewa,
> > >
> > > OK, you have a really big matrix. This implies that somehow you are
> > > referencing many more atoms than you think. Thus I would suggest that
> > you
> > > debug your statement by
> > > Selecting only two residues (pick the simplest ones, such as GLY GLY,
> > then
> > > try GLY ALA), until you understand what atoms are being selected by the
> > > syntax you are using. I have not run this calculation before so I
> can't
> > > debug the statement for you.
> > >
> > > Good luck.
> > >
> > > Sergio Aragon
> > >
> > >
> > > -----Original Message-----
> > > From: Sajeewa Pemasinghe [mailto:sajeewasp.gmail.com]
> > > Sent: Tuesday, June 14, 2011 3:42 PM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] Interpreting the distance covariance matrix
> > >
> > > Hello Aragon,
> > >
> > > There is an offset error in the excel file. The dat file is ok. As you
> > > mentioned earlier I HAVE 53 361 NUMBERS.
> > >
> > > Best Regards
> > >
> > > Sajeewa
> > > On Tue, Jun 14, 2011 at 6:35 PM, Sajeewa Pemasinghe <
> sajeewasp.gmail.com
> > > >wrote:
> > >
> > > > Hi Aragon,
> > > >
> > > > The code I used is this.
> > > >
> > > > matrix distcovar name AS1AS2 out distAS1AS2.dat
> > > >
> > >
> >
> :80,131,154,155,156,174,176,177,178,179,207,310,311,359,426,491,495,497,564,576,609,635.CAoffset100
> > > > analyze matrix AS1AS2 out distAS1AS2anal.dat vecs 0
> > > >
> > > > So I have 22 residue names and I am considering only the alpha
> carbons.
> > > So
> > > > I should only have a 22 by 22 matrix isn't it?
> > > >
> > > > I have attached the resulting matrix file both as a dat file and as
> an
> > > > Excel file. Your help in interpreting the dimensionality of the
> matrix
> > is
> > > > highly appreciated.
> > > >
> > > > Best Regards
> > > >
> > > > Sajeewa
> > > >
> > > >
> > > > On Tue, Jun 14, 2011 at 6:16 PM, Sergio R Aragon <aragons.sfsu.edu>
> > > wrote:
> > > >
> > > >> Hello Sajeewa,
> > > >>
> > > >> Following up on what Mariano Rech has told you, from 22 carbons
> atoms
> > > you
> > > >> would generate a matrix of distances containing 22^2 = 484 numbers.
> > The
> > > >> number of off-diagonal elements for this symmetric matrix is
> > (484-22)/2
> > > =
> > > >> 231. This is equivalent to the formula n(n-1)/2 that Mariano used.
> > > Thus we
> > > >> would believe you have 231 different numbers. That is not at all
> the
> > > same
> > > >> as saying you have a 231 x 231 matrix (that would yield 231^2 = 53
> 361
> > > >> numbers!). How many numbers do you actually have?
> > > >>
> > > >> Cheers,
> > > >>
> > > >> Sergio Aragon
> > > >>
> > > >>
> > > >> -----Original Message-----
> > > >> From: Sajeewa Pemasinghe [mailto:sajeewasp.gmail.com]
> > > >> Sent: Monday, June 13, 2011 3:49 PM
> > > >> To: amber.ambermd.org
> > > >> Subject: [AMBER] Interpreting the distance covariance matrix
> > > >>
> > > >> Hi,
> > > >>
> > > >> I have run a distance-covarinace analysis for 22 alpha carbon atoms
> > > >> specified by the mask1. I thought I would get a 22 by 22 symmetric
> > > matrix
> > > >> where the diagonal elements correspond to the variances. Instead I
> got
> > a
> > > >> 231
> > > >> by 231 symmetric matrix. I am having a very hard time interpreting
> > this.
> > > >> This is my first time running a distance covariance calculation in
> > > amber.
> > > >> I
> > > >> would really appreciate if you could give me some helpful
> explanation
> > in
> > > >> interpreting the structure of 231 by 231 matrix.
> > > >>
> > > >> Best Regards
> > > >> Sajeewa
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Received on Tue Jun 14 2011 - 18:30:03 PDT
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