- 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 19:49:04 -0400

Thank you very much. I'll try to figure it out.

On Tue, Jun 14, 2011 at 7:40 PM, Sergio R Aragon <aragons.sfsu.edu> wrote:

*> 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.CAoffset100
*

*> > 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
*

*>
*

*>
*

*>
*

*> _______________________________________________
*

*> 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 - 17:00:05 PDT

Date: Tue, 14 Jun 2011 19:49:04 -0400

Thank you very much. I'll try to figure it out.

On Tue, Jun 14, 2011 at 7:40 PM, Sergio R Aragon <aragons.sfsu.edu> wrote:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Tue Jun 14 2011 - 17:00:05 PDT

Custom Search