Hi Bipin,
You have three coordinates per residue, hence a 3Nx3N matrix.
Cheers,
Tsjerk
On Jun 25, 2011 4:40 PM, "bipin singh" wrote:
Hello,
I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but
after plotting the correlation, I have observed that it is
of 537X537,instead
Hello,
I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but
after plotting the correlation, I have observed that it is
of 537X537,instead of179X179.Please suggest me how to get correlation
between the C-alpha atoms only.
On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrot
Thanks a lot Sir for your help.
On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote:
> Hi Bipin,
>
> Read them in as a vector of numbers and divide them into sqrt(len(vector))
> rows to get yourself a nice square correlation matrix.
>
> Cheers,
>
> Tsjerk
>
> On Jun 24, 2011 3:28 PM, "bipi
Hi Bipin,
Read them in as a vector of numbers and divide them into sqrt(len(vector))
rows to get yourself a nice square correlation matrix.
Cheers,
Tsjerk
On Jun 24, 2011 3:28 PM, "bipin singh" wrote:
Hello,
I have some doubts regarding the output file correl.dat as it contains 3
columns, but
Hello,
I have some doubts regarding the output file correl.dat as it contains 3
columns, but I am not able to get what are
these column contains,I mean how to change it to the format in which I can
directly plot the data to get DCCM map...
For e.g in this form
Res1 Res2 Correlation coefficient
x
Of course you did... Though mind the brackets :)
C_ij = / sqrt ( * )
The point I want to make is that you can easily take the output from
g_covar -ascii and turn it into a correlation matrix. In R
(r-project.org) there is even a dedicated function for it:
x <- scan("covar.dat")
x <- matrix(x,
Hi,
Thats actualy that i did here [1]. Extracting coordinate for every atom
in interesting two group and computing
C_ij = / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j
is vectors
[1]
http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl
On S
Hey,
The method from Lange is quite a different thing. It includes
non-linear correlations, which is interesting to look at for overall
correlation between atoms. If the ultimate goal is to do PCA on it,
then it will give you awkward components that will give you a hard
time trying to interpret.
Hi.
There is two possibilitys
1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that
compites
general corelation coefficients
2. My utility that computes pearson correlation coefficients [2]
[1]
http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.h
Dear all,
Is there any built in function that gives me the pairwise correlation of the
fluctuation (unit vector between two coordinates of a residue) of residues
(averaged over the input trajectory). I tried g_covar but that's not what
i'm looking for. The result I want should be an NxN matrix wit
Hi,
Well, since interatomic distances are properties of single
conformations and fluctuation covariances/correlations are properties
of sets of conformations, it is simply impossible. You might plot the
covariances/correlations against the mean distances, if you feel you
must. Be sure to use the a
On 16/03/2010 5:16 PM, shahab shariati wrote:
Hi gromacs users
After using g_covar for obtaining dynamic cross correlation map, how is
obtained cross-correlations as a function of interatomic distance?
Thank you so much for any help!
I'm not even sure whether "cross-correlations as a function
Hi gromacs users
After using g_covar for obtaining dynamic cross correlation map, how is
obtained cross-correlations as a function of interatomic distance?
Thank you so much for any help!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
Hi gromacs users
After using g_covar for obtaining dynamic cross correlation map, how is
obtained cross-correlations as a function of interatomic distance?
Thank you so much for any help!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
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