Hi, The only program I know using T1 and T2 instead of R1 and R2 is the Mathematica notebook of Leo Spyracopoulos (JBNMR (2006), 36: 215-224).
Regards, Séb 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? > > 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 <[EMAIL PROTECTED]> 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 >> [email protected] >> >> 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 >> >> >> > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > 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 > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] 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
