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 - 17:30:03 PDT
