# Re: [AMBER] Interpreting the distance covariance matrix

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Tue, 14 Jun 2011 18:35:07 -0400

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.CAoffset
100
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