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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> >>
> >>
> >>
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> >>
> >
> >
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Received on Tue Jun 14 2011 - 17:00:05 PDT
