- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

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
*

*>> _______________________________________________
*

*>> 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

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

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:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

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

Custom Search