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
Re: SH3, model-free failed (relax GUI)