Dear Dr. Edward d'Auvergne, Many thanks for your kind reply. I will carefully take a look at what you suggest!
Best, Yitao > 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 <chem...@ust.hk> 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@gna.org >> >> 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 > Best, Yitao _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
