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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
*

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*

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*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

*>
*

*> _______________________________________________
*

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*

*> AMBER.ambermd.org
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Received on Tue Jun 14 2011 - 16:00:03 PDT

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:

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- application/octet-stream attachment: distAS1AS2.dat

- application/vnd.openxmlformats-officedocument.spreadsheetml.sheet attachment: distAS1AS2.xlsx

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