Dear Yitao, Welcome to the relax mailing lists! My late response is because I have just returned from holidays. To simplify how you use relax, you could try running the relax graphical user interface or GUI (http://www.nmr-relax.com/refs.html#Bieri11): Bieri M., d'Auvergne E. J., Gooley P. R. (2011). relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins. J. Biomol. NMR, 50(2), 147-155. (http://dx.doi.org/10.1007/s10858-011-9509-1) At the command prompt, just type: $ relax --gui This works on all operating systems. How do you wish to perform your model-free analysis? You should note that there are two parts to a model-free analysis. The first part are the basic model-free models to be optimised as well as the diffusion tensor. The second part is a highly iterative protocol for how you should solve the combined and convoluted optimisation and model selection problem. See my review at http://dx.doi.org/10.1039/b702202f for an in depth explanation of this dual concept. There are a number of protocols available for model-free analysis. Almost all can currently be implemented via a relax script using a little Python programming, if you have the ability. However one protocol is already fully implemented for you. This is the new protocol I published in: 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) 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) If you read these two references, which I highly recommend you do, you will see that ideas from the Peter Wright 2004 JBNMR paper are no longer relevant. As the new protocol starts with the internal motion rather than with the diffusion tensor - you do not need an initial diffusion tensor estimate. So all of the extensive literature on correctly finding the initial tensor estimate is no longer of any use. If you use the dauverge_protocol auto-analysis in a script or simply use the GUI, then you will be using this new protocol and you can skip the ideas from the Wright paper. I hope this helps. Regards, Edward On 8 August 2014 06:00, FENG yitao <chemfyt@xxxxxx> wrote:
Dear relax users, I am a new user of the relax and I don't have any background about python. This software seems quite powerful but difficult for me to use. I have collected the T1, T2 and NOE data. Before sending for modelfree calculation, I want to select models residue per residue in order to improve the fitting accuracy as mentioned in P. E. Wright's J.Biomol.NMR paper in 2004 (model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation). So I go to the user manual and after several days I got to know how to input the R1, R2 and NOE data (sorry for my slow learning). When I start to do model-selection, the software needs me to provide diffusion tensor but I don't know how to do this. I wonder whether any of you have any protocol for easy usage of model selection. I'm sorry for my silly question and I am looking forward to your reply. Best, Tom Best, Yitao _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@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-users