Re: numerical cpmg fitRe: numerical cpmg fitHi Paul, I have now implemented step 2 of the tutorial for adding relaxation dispersion models (http://article.gmane.org/gmane.science.nmr.relax.devel/3907, in the commit r20277 at http://article.gmane.org/gmane.science.nmr.relax.scm/18033). This is one aspect that the relax user sees. I have assumed that 'dw' is a parameter of this model - i.e. the Delta_omega chemical shift difference between states A and B. But I am not sure if this is used in your code and if it relates to the fg parameter. Would you know the relationship? Cheers, Edward On 11 July 2013 18:23, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hello, Another question I have is what are the parameters of this model? It relates to the function arguments currently labelled as unknown in the function docstring. I would like to implement step 2 of the tutorial on adding relaxation dispersion models to relax (the relax_disp.select_model user function front end, see http://article.gmane.org/gmane.science.nmr.relax.devel/3907), but I'm not sure how to list the parameters of the model for the user. Is there a population parameter (pA or pB)? Are R2E and R2G the same as the R20A and R20B rates (the R2 rates in the absence of exchange for states A and B for a fixed magnetic field strength)? Cheers, Edward On 11 July 2013 16:14, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:Hi Paul, I have now incorporated this code into relax (see http://article.gmane.org/gmane.science.nmr.relax.scm/18025). Could you please check the code, comments, and docstrings carefully and see if there are any issues? Could you also tell me if anyone else should be included in the copyright notice? It would be useful to replace the 'Unknown' elements in the function docstring with basic descriptions of the parameter and its Python object type. And any suggestions for comments describing in basic NMR terms what the code is doing (the physics of the propagations, for example) would also be appreciated. You can get the new code by typing the following in the base directory of the checked out copy of the relax_disp branch: $ svn up There was an indentation problem that I have tried to solve. Also I cannot determine where the mpower() function comes from - it appears not to be part of numpy or scipy. Is this an outside function you wrote? I have also made a number of significant speed ups of the code (see article.gmane.org/gmane.science.nmr.relax.scm/18029). Note that this cannot be selected as a model in the dispersion analysis yet. Cheers, Edward On 11 July 2013 13:47, Paul Schanda <paul.schanda@xxxxxx> wrote:Hi Edward, Here is a function that does a numerical fit of CPMG. It uses an explicit matrix that contains relaxation, exchange and chemical shift terms. It does the 180deg pulses in the CPMG train with conjugate complex matrices. It returns calculated R2eff values, so it can be used for numerical fitting of CPMG. It is an addition to the functions that I previously sent to you. The approach of Bloch-McConnell can be found in chapter 3.1 of Palmer, A. G. Chem Rev 2004, 104, 3623–3640. I wrote this function (initially in MATLAB) in 2010. I agree that this code is released under the GPL3 or higher licence. Paul def func1(R2E,R2G,fg,kge,keg, cpmgfreq,tcpmg): kex=kge+keg Rcalc_array=np.zeros(len(cpmgfreq)) Rr = -1.*np.matrix([[R2G, 0.],[0., R2E]]) Rex = -1.*np.matrix([[kge,-keg],[-kge, keg]]) RCS = complex(0.,-1.)*np.matrix([[0. ,0.],[0.,fg]]) R = Rr + Rex + RCS cR = np.conj(R) IGeq=keg/kex; IEeq=kge/kex M0=np.matrix([[IGeq],[IEeq]]) for k in range(len(cpmgfreq)): tcp=1./(4.*cpmgfreq[k]) prop_2 =np.dot(np.dot(sci.expm(R*tcp),sci.expm(cR*2.*tcp)),sci.expm(R*tcp)) prop_total =mpower(prop_2,cpmgfreq[k]*tcpmg) Moft = prop_total*M0 Mgx=Moft[0].real/M0[0] Rcalc=-(1./tcpmg)*math.log(Mgx); Rcalc_array[k]=Rcalc return Rcalc_array _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@xxxxxxx To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel