Hi Soumya,
The data look quite convincing. The pattern formed by your order
parameter trace seems to match the patterns in your base R2 and NOE
data. So this is a very good sign. There is a bit more variability
in your order parameters compared to the base data which could
indicate that the bond vector orientations in some parts might be
slightly skewed. But I don't have the base numbers to carefully check
and see it the S2 variability matches trends and variations in your
2-field strength base data - that is something you need to do to be
sure yourself. Any points you find strange, you should go back to the
base relaxation data and your spectra and see if you can see anything
strange (peak overlap or truncation or other artifacts when you drop
noise level to the baseplane). You may find that certain peaks should
not be included. You can also look back at your relax log file and
see if the AIC model selection results are reasonable
(http://dx.doi.org/10.1023/A:1021902006114). Also look at the model
elimination results in the log file
(http://dx.doi.org/10.1007/s10858-006-9007-z). You should also check
in that log for all warning messages to be sure that relax is not
warning you of a major problem.
Anyway, you should be pretty close to having your final analysis and
publishable data (after carefully auditing all your data points).
Don't forget the BMRB export using the 'File->Export for BMRB
deposition' menu item and BMRB submission via the ADIT-NMR system at
http://www.bmrb.wisc.edu/deposit/ for the data you will publish - so
that you have a BMRB deposition number for your paper. For citing
relax, you could use the compact single citation notation for the
back-to-back publication as - d'Auvergne, E. J. and Gooley, P. R.
(2008). Optimisation of NMR dynamic models. J. Biomol. NMR, 40(2),
107-133.
Regards,
Edward
On 11 April 2014 07:26, Soumya <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Follow-up Comment #2, sr #3127 (project relax):
Hi Edward,
The Lipari-Szabo order parameter calculations went to plan and the results
mostly look like they should. I am quite curious about sudden drops in the
S2
values (see attached "S2 only Eddie"; relevant columns highlighted in red).
I
have a structure that has very short secondary structure elements separated
by
intervening loops. For example, beta hairpin followed by a transient helix.
The excursions in S2 correspond to these loops. Do these sudden drops in S2
make sense in the context of what I have described? Or are they unusual in
your experience?
I guess this all comes about since I have not done any model-free analysis
before and don't have a feel for what these data should look like given a
particular structure. By looking at a Google image search my data seem okay,
but I'd rather have an expert opinion from you.
Cheers,
Soumya
(file #20505)
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Re: [sr #3127] Opposite S2 values to expected