Hello,<br>I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are<br>these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map...<br>
For e.g in this form<br>Res1 Res2 Correlation coefficient<br>x y z<br><div class="gmail_quote">On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Of course you did... Though mind the brackets :)<br>
<div class="im"><br>
C_ij = <x_i * x_j> / sqrt ( <x_i ^2> * <x_j^2> )<br>
<br>
</div>The point I want to make is that you can easily take the output from<br>
g_covar -ascii and turn it into a correlation matrix. In R<br>
(<a href="http://r-project.org" target="_blank">r-project.org</a>) there is even a dedicated function for it:<br>
<br>
x <- scan("covar.dat")<br>
x <- matrix(x,sqrt(length(x)))<br>
y <- cov2cor(x)<br>
write(y,"correl.dat",ncolumns=3)<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov<br>
<div><div></div><div class="h5"><<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
> Hi,<br>
><br>
> Thats actualy that i did here [1]. Extracting coordinate for every atom in<br>
> interesting two group and computing<br>
><br>
> C_ij = <x_i * x_j> / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is<br>
> vectors<br>
><br>
><br>
> [1]<br>
> <a href="http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl" target="_blank">http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl</a><br>
> On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote:<br>
>><br>
>> Hey,<br>
>><br>
>> The method from Lange is quite a different thing. It includes<br>
>> non-linear correlations, which is interesting to look at for overall<br>
>> correlation between atoms. If the ultimate goal is to do PCA on it,<br>
>> then it will give you awkward components that will give you a hard<br>
>> time trying to interpret.<br>
>><br>
>> There is another way, besides using an external tool. Extract the<br>
>> diagonal elements and take the square root of each. Then for each<br>
>> element [i,j] in the matrix, divide by the elements i and j of these<br>
>> square roots, and you'll have yourself a correlation matrix.<br>
>><br>
>> Hope it helps,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov<br>
>> <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
>>><br>
>>> Hi.<br>
>>><br>
>>> There is two possibilitys<br>
>>> 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that<br>
>>> compites<br>
>>> general corelation coefficients<br>
>>> 2. My utility that computes pearson correlation coefficients [2]<br>
>>><br>
>>> [1]<br>
>>><br>
>>><br>
>>> <a href="http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html" target="_blank">http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html</a><br>
>>> [2]<br>
>>><br>
>>><br>
>>> <a href="http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl" target="_blank">http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl</a><br>
>>><br>
>>><br>
>>> On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote:<br>
>>>><br>
>>>> Dear all,<br>
>>>><br>
>>>> Is there any built in function that gives me the pairwise correlation<br>
>>>> of the fluctuation (unit vector between two coordinates of a residue)<br>
>>>> of residues (averaged over the input trajectory). I tried g_covar but<br>
>>>> thats not what im looking for. The result I want should be an NxN<br>
>>>> matrix with values ranging from -1 to 1.<br>
>>>><br>
>>>> Thanks in advance,<br>
>>>> Nihal<br>
>>>><br>
>>>> --<br>
>>>> Elif Nihal Korkmaz<br>
>>>><br>
>>>> Research Assistant<br>
>>>> University of Wisconsin - Biophysics<br>
>>>> Member of Qiang Cui & Thomas Record Labs<br>
>>>> 1101 University Ave, Rm. 8359<br>
>>>> Madison, WI 53706<br>
>>>> Phone: 608-265-3644<br>
>>>> Email: <a href="mailto:korkmaz@wisc.edu">korkmaz@wisc.edu</a> [1]<br>
>>>><br>
>>>><br>
>>>><br>
>>>> Links:<br>
>>>> ------<br>
>>>> [1] mailto:<a href="mailto:korkmaz@wisc.edu">korkmaz@wisc.edu</a><br>
>>><br>
>>> --<br>
>>> Best Regards,<br>
>>> Alexey 'Alexxy' Shvetsov<br>
>>> Petersburg Nuclear Physics Institute, Russia<br>
>>> Department of Molecular and Radiation Biophysics<br>
>>> Gentoo Team Ru<br>
>>> Gentoo Linux Dev<br>
>>> mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
>>> mailto:<a href="mailto:alexxy@gentoo.org">alexxy@gentoo.org</a><br>
>>> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
>>> --<br>
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>>><br>
>><br>
>><br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> post-doctoral researcher<br>
>> Molecular Dynamics Group<br>
>> * Groningen Institute for Biomolecular Research and Biotechnology<br>
>> * Zernike Institute for Advanced Materials<br>
>> University of Groningen<br>
>> The Netherlands<br>
><br>
> --<br>
> Best Regards,<br>
> Alexey 'Alexxy' Shvetsov<br>
> Petersburg Nuclear Physics Institute, Russia<br>
> Department of Molecular and Radiation Biophysics<br>
> Gentoo Team Ru<br>
> Gentoo Linux Dev<br>
> mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>
> mailto:<a href="mailto:alexxy@gentoo.org">alexxy@gentoo.org</a><br>
> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>
> --<br>
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><br>
<br>
<br>
<br>
</div></div>--<br>
<div class="im">Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><span style="color:rgb(51, 51, 255)">-----------------------</span><br style="color:rgb(51, 51, 255)"><i><span style="color:rgb(51, 51, 255)">Regards,</span></i><br style="color:rgb(51, 51, 255)">
<span style="color:rgb(51, 51, 255);font-family:garamond,serif">Bipin Singh</span><br><br>