# Re: [AMBER] Interpreting the distance covariance matrix

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Tue, 14 Jun 2011 18:42:22 -0400

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.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
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Received on Tue Jun 14 2011 - 16:00:06 PDT
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