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 < vmsrvign...@gmail.com> 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 <jalem...@vt.edu>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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists