Hi, I'll answer below:
Values are S2 values just for a sample.
Ok, so this must be the s2.txt file relax produces at the end of the auto-analysis. I'm guessing you opened this file, and not the s2f.txt and s2s.txt file in MS Windows using the results viewer window of the relax GUI. Are these assumptions correct?
I did not use relax to get r1,r2 and noe but used NMRDraw text output, so all data is in text.
Is relax reading these rates correctly, i.e. do you see any warnings when loading the relaxation data? Do the errors you get from NMRDraw match the errors of other programs (using relax for example)?
I copied dauvergne protocol and modified it with my own data set and then on "gui", just followed each step, no problems with "gui" following.
Please keep these separate. A bug or problem in the GUI is not a bug or problem in relax's scripting mode. If you have a problem with the script, please say that you are running the script and the problem is with the script. If you have a problem with the GUI, then state that you are using the GUI and not the scripting mode. The switching between both or not saying which you are using is confusing me.
Rex values seem to correlate a bit with Palmers modelfree4 i executed perfectly but relax is more robust and can perform complete anisotropic which modelfree from Palmer cannot.
The Rex correlation depends on the protocol used not the program. Always remember that relax can produce identical results to Modelfree4, and that if you modify the source code and recompile Modelfree4 it can produce results similar to relax (not identical because there is no choice of high quality optimisation algorithms in Modelfree4). The major difference is that relax supports the ellipsoidal diffusion tensor whereas Modelfree4 does not.
so i used relax to gain more understanding.
For an even deeper understanding, you should look at Sebastien Morin's consistency testing code in relax (http://www.nmr-relax.com/manual/Consistency_testing.html) as well as the reduced spectral density mapping (http://www.nmr-relax.com/manual/Reduced_spectral_density_mapping.html). I would also recommend looking at all the references in the 'Citations' chapter of the relax manual (http://www.nmr-relax.com/manual/Citations.html, though the links are currently broken so the PDF manual http://download.gna.org/relax/manual/relax.pdf would be better).
Relax result of Rex values also correlates with cpmg results but i want to gain more information how to extract data for presentation like i want to know distribution of residues per model.
This is a good sign that the model-free Rex values are not due to a problem with the diffusion tensor! If the diffusion tensor is incorrect, you can see either artificial Rex values or artificial nanosecond motions (see http://dx.doi.org/10.1039/b702202f for a detailed description of this problem). Note that because you have multiple nested and non-nested, yet related, models in a model-free analysis, comparing which model has been selected is physically meaningless. It has more to do with your experimental errors and the quality of your data! The model selected is only interesting from a statistical point of view and not from a dynamics point of view. To understand the motions of your system, it is much better to look at the dynamics itself independent of the models selected.
my structure looks "prolate" but how to tell with relax? i saw it chooses "prolate" for which am happy.
When using the auto-analysis which implements the model-free protocol that I derived (see my 2007 and 2008 papers, http://www.nmr-relax.com/refs.html), then you will see the file: final/tensor.pdb If you are using the GUI, you can see it in the results viewer window. Just open this file from the results viewer and it will open up in PyMOL with your molecule. If you are using the scripting mode, then in the prompt or script after the analysis, you can see the same by typing: pymol.view() pymol.cartoon() pymol.tensor_pdb(file="tensor.pdb", dir="final") I hope some of this helps. Regards, Edward