Hi,
I've had a look at the fields and have a few questions as to how these
should be implemented. I'm assuming that these are the fields for
simply depositing R1 relaxation data into the BMRB, is this correct?
So the first question I have has to do with Rx versus Tx. Almost all
theories for the interpretation of the T1 relaxation times are
dependent upon this being in the R1 rate form (with units of
rad.s^-1). relax (http://nmr-relax.com), Art Palmer's curvefit
(http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software.html),
David Fushman's RELAXFIT
(http://gandalf.umd.edu/FushmanLab/pdsw.html), and almost all other
programs calculate the Rx relaxation rate errors and not relaxation
time errors via Monte Carlo simulation. Then the programs relax
(http://nmr-relax.com), modelfree4
(http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software.html),
dasha (http://www.nmr.ru/dasha.html), DYNAMICS
(http://gandalf.umd.edu/FushmanLab/pdsw.html), Tensor2
(http://www.ibs.fr/ext/labos/LRMN/softs/welcome.htm), etc. all work
with the rates and not the times. So the storage of relation times
and their errors may not be very useful. Is it possible to deposit
rates and their errors rather than the antiquated relaxation times and
their errors? Also, conversion of the Rx relation rate errors to the
Tx time errors would require full Monte Carlo simulation to be
accurate, and I'm not sure if anyone would have done this properly. I
could be wrong (anyone on this list who knows otherwise, please
correct me), but I don't think there are any programs that use the Tx
times or that properly convert Rx errors to Tx errors and vice versa.
The second question I have has to do with the integration of relax
with the BRMB deposition and automating the process. Can all data for
a model-free analysis be deposited at once? For example if relax was
to create a STAR formatted file with the ADIT-NMR fields with the R1,
R2, and NOE values and errors at multiple fields, with the S2, S2f,
S2s, te, ts, tf, and Rex parameters and errors, the selected model
information (model name or parameters of the model), parameters such
as the CSA value used and bond length, and global parameters such as
the diffusion tensor, could this file be accepted? Or will this
require multiple small files for multiple deposition?
I've also noticed from some of the deposited data (e.g.
http://www.bmrb.wisc.edu/data_library/gen_saveframe.php?accNum=6470&saveframe=T1_relaxation
) that all the data is identified by residue number. For supporting
analyses using nucleic acids, small biomolecules, or proteins where
more than just the backbone NH relaxation has been studied, would it
be possible to additionally have an atom or spin numerical code and
textual label? If an analysis is done on a molecular complex, is the
deposition of data for multiple molecules supported as well?
I still have many questions about the fields, their format in the STAR
file to deposit, which are compulsory, and which fields do not yet
exist for deposition of all model-free data (much of this data can be
seen in the relax results file
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
). For example most of the STAR tags in
http://www.bmrb.wisc.edu/data_library/gen_saveframe.php?accNum=5841&saveframe=S2_parameters
are not in the excel spreadsheet. And why are order parameters and
their errors input using the STAR format tags '_S2_value' and
'_S2_error' whereas the T1 fields are called '_T1_value' and
'_T1_value_error' and the effective model-free internal correlation
time te filed under '_Tau_e_value' and '_Tau_e_value_fit_error'?
Would you have an example deposition text file formatted correctly
using the ADIT-NMR tags in the Excel file? Or is this unmodified, for
example is
http://www.bmrb.wisc.edu/cgi-bin/explore.cgi?format=raw&bmrbId=5841
the same file as that that the authors deposited? And how is the
field strength dependent data handled, e.g. in
http://www.bmrb.wisc.edu/cgi-bin/explore.cgi?format=raw&bmrbId=4970
there are 2 spectrometers declared to be a 600 and 750, yet there is
relaxation data at 500, 600 and 750 present in the file?
Cheers,
Edward
P.S. For reference, this message will soon appear at
https://mail.gna.org/public/relax-devel/.
On Mon, Jul 28, 2008 at 6:01 PM, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
Hi Edward,
Sorry for the delay in providing a list of the required ADIT-NMR fields. An
Excel file with the information is attached compiled by one of our
students.
The table provides a fairly complete description of the field and where
appropriate the dependencies on other fields. In terms of the experimental
data, only the fields required for T1 relaxation data were included. The
required fields may vary slightly depending on the kinds of data being
deposited.
I hope this information helps. If you have any questions or need additional
information, please let me know.
All the best,
Eldon
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Re: Required fields in ADIT-NMR