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 _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@xxxxxxx 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-devel