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From: Edward d'A. <ed...@do...> - 2012-01-31 15:45:54
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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 <dha...@do...> 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 > rel...@do... > > 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 |
