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From: Mariano Rech <mariano.rech.gmail.com>

Date: Wed, 15 Jun 2011 02:22:03 +0200

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
*

*> > >> _______________________________________________
*

*> > >> 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
*

*> > >>
*

*> > >
*

*> > >
*

*> > _______________________________________________
*

*> > 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
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

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*

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Received on Tue Jun 14 2011 - 17:30:03 PDT

Date: Wed, 15 Jun 2011 02:22:03 +0200

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>

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Received on Tue Jun 14 2011 - 17:30:03 PDT

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