Hi Dhanas, I would suggest this for the greater scientific worth of the data as well ;) Remember to use temperature calibration with MeOH or DSS for every single experiment. And to use temperature compensation or single scan interleaving for acquisition.
Regards, Edward On 1 February 2012 17:33, Dhanasekaran Muthu <[email protected]> wrote: > Dear Edward, > > Thanks so much for your detailed mail regarding the steps involved in > model-free analysis using single magnetic field data. To harness the > potential of relax-GUI, I am seriously considering doing the experiments in > another field. > > Thanks for your support. > > with best regards, > > Dhanas Muthu > > > > On Jan 31, 2012, at 7:45 AM, Edward d'Auvergne wrote: > >> Dear Dhanas, >> >> Welcome to the relax mailing lists. Thank you, but note that this >> program is the work of a number of relax developers. You are correct >> that you cannot use the GUI for single field strength data. For such >> data, you have to revert to the ancient methodology in the Mandel, >> Akke, and Palmer 1995 paper. This will require scripting, but >> fortunately most of the scripts are already there for you, just not >> fully automated. >> >> To perform this old-style analysis, this will require an initial >> diffusion tensor estimate which you can obtain from relax by setting >> all spins to model m0 and optimising the diffusion tensors (once for >> spherical diffusion, for the prolate spheroid, the oblate spheroid, >> and the ellipsoid). This approximates the R1/R2 ratio methods, but >> has the advantage of not having to convert between the >2000 Euler >> angle conventions/symmetries, etc. which are different between >> Modelfree4, Tensor2, Dasha, and relax. Note you cannot simply take a >> tensor from one program and use it in another, as all programs use >> different Euler or spherical angle notations. There is no sample >> script for this, so you will need to write it yourself. >> >> The next part is iterative. You need to fix the diffusion tensor and >> optimise the model-free models (i.e. the mf_multimodel.py script). >> Then you need to select the best model (the >> sample_scripts/model_free/modsel.py script). And finally you have to >> optimise the diffusion tensor again (this will require your own script >> as there is no equivalent sample script). Using this final diffusion >> tensor as a starting point, you need to repeat all the steps of >> model-free model optimisation, model selection, and tensor >> optimisation until convergence (identical chi-squared values for the >> final optimisation). >> >> What you'd like to do will require script editing and writing on you >> behalf. You will need extensive use of the user function >> documentation in the manual. I do not believe anyone has used relax >> to perform such an analysis for a long, long time (I could be wrong >> though). Most scripts for this would be for the old relax version >> 1.0.x or earlier, so they cannot be used with modern versions of >> relax. This Mandel et al methodology is heading towards being two >> decades old - it is a very ancient technique with many known and >> documented problems which you will need to be very aware of! I >> suggest starting with my review: >> >> d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the >> model-free problem and the diffusion seeded model-free paradigm. Mol. >> Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f) >> >> Or my paper: >> >> d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR >> dynamic models II. A new methodology for the dual optimisation of the >> model-free parameters and the Brownian rotational diffusion tensor. J. >> Biomol. NMR, 40(2), 121-133. >> (http://dx.doi.org/10.1007/s10858-007-9213-3). >> >> The review covers most of the problems, and the 2008 paper shows an >> example where such methodology clearly fails. To perform a single >> field strength analysis, you need to be acutely aware of these >> problems. If you have any problems with all of the scripting, please >> don't hesitate to ask on the mailing list. I hope this helps. >> >> Regards, >> >> Edward >> >> >> P. S. Collecting data at 2 or more field strengths (essentially with >> both per-experiment temperature calibration and temperature >> compensation) will allow you to avoid scripting and use the automated >> analysis via the GUI. >> >> >> >> >> On 30 January 2012 19:53, Dhanasekaran Muthu <[email protected]> wrote: >>> First, I wanted to thank for creating such a wonderful program for >>> mode-free analysis. Using the recent version with GUI, I was able to get >>> T1, T2 and NOE values without much effort. But I am not able to proceed >>> further to do the mode-free analysis because the relax needs more than one >>> filed frequency data. My problem is that I have data from only one >>> frequency and I do not know the sequence of steps involved in running the >>> relax. I learned from the forum that this has been asked several times and >>> answered several times. I am also aware of problems with single frequency >>> data. But I have to work with only one frequency data for the time being. >>> Even after reading the forum and well-detailed manual, I am not able to >>> understand what are the steps I should be doing to get model-free data. My >>> understanding so far is i) first run mf-multimodel.py and then ii) >>> modesel.py after removing the models M4 to M9. It would be nice if some one >>> post the details of how to use relax for single frequency data, if they >>> were successful already running the calculations. I would like to connect >>> with those people who are in my situation and created successful code for >>> running relax. >>> >>> Thanks, >>> >>> Dhanas Muthu >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> [email protected] >>> >>> 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-users > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > 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-users _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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-users
