Hi Vignesh, If your covariances show different ranges, isn't that a difference between your systems, wild-type and mutated? Then again, there's also noise in the covariances (noise in the fluctuations, ergo noise in the noise ;)). The rest might be comparable, making scaling based on the extremes seem like a bad idea. You might be better of calculating correlations, rather than covariances. There's a modified g_covar in the contributions section of the gromacs site for calculating those.
Cheers, Tsjerk On Thu, Nov 11, 2010 at 3:53 AM, Vigneshwar Ramakrishnan <[email protected]> wrote: > Dear All, > I tried using the xpm2ps -combine option to plot the two matrices in the > same plot. > "xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves > -cmin -0.5 -cmax 0.8" > > However, I still get two legends and each of the matrices are scaled > differently. That is, the output range is NOT combined, as the -combine > option is supposed to do. I tried different options (add, sub, div ; with > and without the -cmin and -cmax options etc) > I am sure I am missing something here. May I please know if anybody got it > worked, and if so, can help me out? > Thanks very much, > Vignesh > On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan > <[email protected]> wrote: >> >> Thanks very much, Justin. Somehow this thread did not come up during my >> search. >> Really appreciate your help. >> Sincerely, >> Vignesh >> >> On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul <[email protected]> >> wrote: >>> >>> There are two relevant threads on this same topic that will likely >>> provide some insight (particularly the second): >>> >>> http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html >>> http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html >>> >>> -Justin >>> >>> Vigneshwar Ramakrishnan wrote: >>>> >>>> Dear All, >>>> I am trying to study the effect of single-point mutations on correlated >>>> motions in a protein-DNA system. I am able to calculate the atomic >>>> covariance matrix using the g_covar -xpma option. However, when I try to >>>> compare the covariance matrices for the two systems (to study the effect of >>>> the mutation), I find that the output is not scaled identically. That is, >>>> in >>>> one of the systems the atomic covariance varies between -0.04 and +0.5 >>>> whereas in the other it varies between -0.1 and +0.4. Now, this means that >>>> I >>>> cannot compare the two systems immediately from the eps file output >>>> (obtained after xpm2ps). >>>> Could anybody please tell me if there is a way to plot the output on >>>> identical scales (say, -1 to +1, or any other scale) using GROMACS? >>>> The other way, I understand is to use the ascii output of g_covar and >>>> use the values to create the covariance plot using softwares like MATLAB >>>> which can rescale the image colors. However, for this, one needs to >>>> calculate the atomic covariance from the ascii output (which is >>>> x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to >>>> calculate >>>> atomic covariance is "for each atom pair the sum of the xx, yy and zz >>>> covariances". Am I right if I understand that this means: >>>> atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + >>>> z2z2 ... >>>> I greatly appreciate any help or pointers. >>>> Thanks very much, Sincerely, Vignesh >>>> >>>> >>>> -- >>>> R.Vigneshwar >>>> Graduate Student, >>>> Dept. of Chemical & Biomolecular Engg, >>>> National University of Singapore, >>>> Singapore >>>> >>>> "Strive for Excellence, Never be satisfied with the second Best!!" >>>> >>>> I arise in the morning torn between a desire to improve the world and a >>>> desire to enjoy the world. This makes it hard to plan the day. (E.B. White) >>>> >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> R.Vigneshwar >> Graduate Student, >> Dept. of Chemical & Biomolecular Engg, >> National University of Singapore, >> Singapore >> >> "Strive for Excellence, Never be satisfied with the second Best!!" >> >> I arise in the morning torn between a desire to improve the world and a >> desire to enjoy the world. This makes it hard to plan the day. (E.B. White) > > > > -- > R.Vigneshwar > Graduate Student, > Dept. of Chemical & Biomolecular Engg, > National University of Singapore, > Singapore > > "Strive for Excellence, Never be satisfied with the second Best!!" > > I arise in the morning torn between a desire to improve the world and a > desire to enjoy the world. This makes it hard to plan the day. (E.B. White) > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
