Hi,
Thank you for the quick response and feedback. I will try to answer as many
of your comments and questions below. We are converting all of our data from
NMR-STAR v2.1 to NMR-STAR v3.1. Examples of the v3.1 files can be found on
the BMRB ftp site at
ftp://ftp.bmrb.wisc.edu/pub/data/nmr-star-v3/
These are early beta files and may have serious problems.
For the purposes of this discussion, I will be referring to v3.1 tags.
Descriptions for these tags can be found at this URL:
http://www.bmrb.wisc.edu/formats.html
Files containing a fake NMR-STAR v3.1 file (nmrstar3_fake.txt) and other
information on the dictionary in its 'working' form is available from the
BMRB ftp site:
ftp://ftp.bmrb.wisc.edu/pub/data/nmr-star_dict/dictionary_files
We are very open to suggestions from the community on how to model and
capture relaxation data and are quite excited about this discussion. I am
sure I have not addressed all of your questions, but I hope this is a start.
Cheers,
Eldon
Edward d'Auvergne wrote:
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?
The Excel file contains the tags for the fields in the ADIT-NMR deposition
system that are mandatory. These fields represent for the most part the meta
information about the molecule, sample, sample conditions, spectrometers,
etc. The T1 fields were included as an example for one kind of relaxation
data and the mandatory fields that would need to be entered in ADIT-NMR. The
actual tables of data would be uploaded at the time of deposition.
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?
Yes, you can deposit rates and the appropriate error and not the times. The
T1.Val and T1.Val_err tags can have units of appropriate for either times or
rates (i.e., s or s-1). In the header to the table of T1 values is a tag
_Heteronucl_T1_list.T1_val_units. The value to this tag defines whether the
T1 data have been expressed as times or rates.
The terminology used for relaxation studies in NMR has been quite diverse.
At the time these tags were constructed, the term 'T1' still seemed to be
the most commonly used. But, we realized capturing the data as rates was
extremely important and so we allowed for the units for the values to
actually determine if the values were times or rates.
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?
All of the data can be uploaded as one file. The NMR-STAR format is modular
and a single file can contain as many modules (saveframes) of the same or
different type with a few exceptions. A module or saveframe begins with the
key term 'save_somestring' and ends with the key term 'save_'. A file can
contain as many R1, R2, and NOE modules as needed. Within each of the
modules there is a header tag that takes as a value the field strength of
the spectrometer used to collect the data in that module as well as the NMR
experiment. It is important that the experiment used for the data be defined
uniquely.
The following list of tags contains most of the values you mention, S2, S2f,
S2s, te, ts, Rex all with errors, and type of model fit. It is missing the
tf, but this can be easily added. The units for te and ts are provided in
the header tags
_Order_parameter_list.Tau_e_val_units and
_Order_parameter_list.Tau_s_val_units. For the order parameter data, it is
important to include the experiments used to collect the underlying data. In
this way the order parameters are linked to the R1, R2, etc data used in
doing the fitting. It is possible to include in the file a description of
the software used and the 'method' or parameter file.
_Order_param.Order_param_val
_Order_param.Order_param_val_fit_err
_Order_param.Tau_e_val
_Order_param.Tau_e_val_fit_err
_Order_param.Rex_val
_Order_param.Rex_val_fit_err
_Order_param.Model_free_sum_squared_errs
_Order_param.Model_fit
_Order_param.Sf2_val
_Order_param.Sf2_val_fit_err
_Order_param.Ss2_val
_Order_param.Ss2_val_fit_err
_Order_param.Tau_s_val
_Order_param.Tau_s_val_fit_err
_Order_param.SH2_val
_Order_param.SH2_val_fit_err
_Order_param.SN2_val
_Order_param.SN2_val_fit_err
The CSA data would be included in a separate module, but the same file.
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?
The header tag of the type '_Heteronucl_T1_list.T1_coherence_type' is
intended to provide an idea of the coherence being measured. In addition,
the following set of tags or similar set for other kinds of data are
provided for every row in a data value table. The values for these tags
allow an atom within a molecular assembly of almost any complexity
(including ones that are undergoing chemical or conformational exchange) to
be defined.
_T1.Entity_assembly_ID
_T1.Entity_ID
_T1.Comp_index_ID
_T1.Seq_ID
_T1.Comp_ID
_T1.Atom_ID
_T1.Atom_type
_T1.Atom_isotope_number
The data that is available from BMRB has been supplied by authors for the
most part and the quality and how well the data are described is variable
and in all cases out of our control as authors do not respond to our
requests for better descriptions and more complete data sets.
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'?
When working on an almost 5000 tag dictionary over many years,
inconsistencies creep into the tag names. We have tried to eliminate these
inconsistencies as much as possible in the NMR-STAR v3 dictionary, but I
would guess there are still at least a few.
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?
I do not have a full relaxation example file. For example files you should
look in the directory on the ftp site listed above. We are working to clean
up these files as quickly as possible.
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?
As mentioned above, for each module containing data that are field strength
dependent there should be a tag that takes as a value the field strength of
the spectrometer used to collect the data. For data like order parameters
that are derived from different sets of data, currently the experiment list
is used to trace back to the input data and spectrometer field strength.
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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BMRB NMR-STAR v3.1 file format or STAR format reader/writer (maybe using CCPN?).