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From: Sergio R Aragon <aragons.sfsu.edu>

Date: Tue, 14 Jun 2011 23:40:41 +0000

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.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
*

*>>
*

*>
*

*>
*

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Received on Tue Jun 14 2011 - 17:00:03 PDT

Date: Tue, 14 Jun 2011 23:40:41 +0000

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:

_______________________________________________

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

Received on Tue Jun 14 2011 - 17:00:03 PDT

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