Hi, >> I would recommend reading Sebastien Morin's paper about the >> consistency testing to understand how to interpret the plots. He also >> gives the relevant references for the different parts of the tests >> where you will find more details. I would recommend it. > > Yes, of course I read the paper. But since the SH3 is such a small protein > with a correlation time far less then the 5 ns mentioned in the paper, I'm > not sure about the reliability of the results. From the interpretation of the > correlation plots and the "J(0)-test" the data seem to be consistent.
I remember this limit, though I thought is was only for a subset of the tests. I can't remember exactly, it was a long time ago that I read all these papers. >> As for the >> model elimination, this is completely explained in my 2006 paper on >> model-free model elimination >> (http://dx.doi.org/10.1007/s10858-006-9007-z). > > Thank you for the hint. I should have just printed out and read each and > every paper of yours. Reading my thesis (http://www.amazon.com/Protein-Dynamics-Model-free-Analysis-Relaxation/dp/3639057627) might be easier :P >> Now that I looked more carefully at >> the results file, I can see the exact problem. I would recommend >> multiplying your proton frequencies by 1e6, as they should be in Hz ;) > > Great news! :D Thank you so much for the hint. I'll start relax once more > with correct frequency values. You should see something quite different! > Something that's bugging me anyway, and I should probably file a bug report > for: There is no convenient or obvious way how to edit the relaxation data > loaded into the MF auto-analysis. I'm currently working on a relax branch (http://svn.gna.org/viewcvs/relax/branches/uf_redesign/) in which core parts of relax are being completely redesigned for speed and flexibility. Once complete, this will be merged back into the main line, and then relax 1.4.0 (or maybe 2.0.0) will be released. This will add all of the flexibility of the prompt and scripting user interfaces into the GUI. This may enable the flexibility you require. Though this would be to simply delete the relaxation data and reload it. Otherwise, an option would be to suggest a few basic user functions which would do what you need (and maybe even try to add them yourself). > Also, deleting NOE data sets is failing here: > > relax> relax_data.delete(ri_id='noe.600') > Traceback (most recent call last): > File "/usr/local/relax/gui/interpreter.py", line 311, in run > apply(fn, args, kwds) > File "/usr/local/relax/prompt/relax_data.py", line 128, in delete > relax_data.delete(ri_id=ri_id) > File "/usr/local/relax/generic_fns/relax_data.py", line 484, in delete > del spin.ri_data[ri_id] > KeyError: 'noe.600' > > I guess this is some kind of bug. The error message is not telling so much. > You can try for yourself by opening the "mf_state.bz2" file in the dropbox > folder. This looks like it is actually a problem with the updating of the relaxation data list GUI element, and I'm guessing you tried to delete the data twice? If you could submit a bug report for this, I will then fix this problem. Cheers, Edward _______________________________________________ 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
