Hi, Sorry, I'm not exactly sure what the graphs correspond to. Is 't-rex-sim.agr' Modelfree4 using the prolate (or oblate) spheroid (this is axially symmetric anisotropic Brownian rotational diffusion)? And is 't-rex-relax.agr' the results from relax using the spheroid tensor? Have you used constraints on Da in relax to isolate the oblate and prolate spheroids? Also how many iterations of the model-free optimisation; model elimination; model selection; and global minimisation (the optimisation of the model-free parameters of all spin systems together with the diffusion parameters) have you used? What is the input data and do you have data at more that one field strength? I'll try to answer some of your questions, but without more information these may not be the answers you are after. The first thing which is a little worrying is that in 't-rex-sim.agr' there are many ts values between 6 to 8 nanoseconds. Unless you are working with an unfolded protein or a system that is far from globular, this is a very strong indication that the diffusion tensor is significantly underestimated. How did you determine the initial diffusion tensor in the analyses? Did you use the full_analysis.py script when using relax (which requires data at minimally 2 field strengths)? The errors on the Modelfree ts results are also worrying. This, to me, looks like that there has been failures in the MC simulations causing very similar errors on all the high ts values. Did you use an upper limit of 10 ns in Modelfree? Another worry is that you obtained similar results from relax using the spherical and spheroidal diffusion! How many iterations of model-free analysis did you use? And how did you determine the initial diffusion tensor? As for the te values in the nanosecond range, this is perfectly normal. This is modelling slow internal motions. Model m5 was designed for this purpose, but if the fast internal motion is close to insignificant due to experimental noise, then model m2 is perfectly capable in modelling the slow motion. Also if you set the range of the y-axis in all the correlation time graphs from 0 to 10 ns, then you can see that the results from Modelfree4 are more worrying. For the correlation time results, it is better to make two graphs - one for fast motions up to 200 or so picoseconds and one for slow motions from 200 ps up. Don't forget that what you are doing is modelling. The models don't care what the underlying true dynamics are - they will model that motion as best as they can. So classifying the dynamics based on which model is selected is at best distracting or at worst misleading. It's the results that matter, not the model. I hope this answers some of your questions. Regards, Edward On 8/8/07, Hongyan Li <hylichem@xxxxxxxxxxxx> wrote:
Dear relax users, I have tried to simulate my dynamic data using isotropic and axial symetric model in both relax and modelfree which gave rise to a very different results. The relax used more M2 and M4 models but gave rise to strange "te" values as big as "ts" (in M5 model). Please see the attached which are the graphs generated using data obtained from both modelfree and relax using same set of data. There must be something wrong. The results from relax are a bit weird and similar results were obtained uing axially symmetric model. Any suggestion will be highly appreciated! Hongyan Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong _______________________________________________ relax (http://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