Hi Mengjun, All of your questions are answered by the literature behind this analysis. There are three key references as stated in chapter 2 of the relax manual:
- Fushman, D., Tjandra, N., and Cowburn, D. (1999). An approach to direct determination of protein dynamics from 15N NMR relaxation at multiple fields, independent of variable 15N chemical shift anisotropy and chemical exchange contributions. J. Am. Chem. Soc., 121(37), 8577–8582. (10.1021/ja9904991) - Farrow, N. A., Zhang, O. W., Szabo, A., Torchia, D. A., and Kay, L. E. (1995). Spectral density-function mapping using N-15 relaxation data exclusively. J. Biomol. NMR, 6(2), 153–162. (10.1007/bf00211779) - Fushman, D., Tjandra, N., and Cowburn, D. (1998). Direct measurement of 15N chemical shift anisotropy in solution. J. Am. Chem. Soc., 120(42), 10947–10952. (10.1021/ja981686m) After reading these you should understand what is happening and why tc is very important (you really should read the base literature for any analysis you perform). I am assuming you have read Sebastien's paper, if not then you must follow the link http://dx.doi.org/10.1007/s10858-009-9381-4. And the value of 15.7 is the angle you seek. If you want to change this angle, then be sure that you fully understand all of the contents of the 4 above referenced papers. Regards, Edward On 4 April 2013 16:48, <[email protected]> wrote: > Hi, > > Thank you very much for your email. One question about the > consistency_tests.py file, when using consistency_tests.py to extract J (0) > from one field strength data R1/R2/NOE, following parameter is needed to > set: > > # Set the angle between the 15N-1H vector and the principal axis of the 15N > chemical shift tensor > value.set(val=15.7, param='orientation') > > # Set the approximate correlation time. > value.set(val=13 * 1e-9, param='tc') > > When using consistency_tests.py, how to set the angle between the 15N-1H > vector and the principal axis of the 15N chemical shift tensor ? perhaps, > val=15.7 ? And the correlation time is also needed to set, I am confused > about setting the global correlation time before a complete model free > analysis since the global correlation time can be extracted after the > complete model free analysis. > > However, in jw_mapping.py, which can also be used to exctract J (0), no such > parameter is needed to set ? > > > Thank you. > > With best regards, > > Mengjun > > > > > > > Quoting Sébastien Morin <[email protected]>: > >> Hi, >> >> Indeed, as Edward pointed, the consistency testing procedure involves two >> steps, the first one being to load data from each magnetic field separately >> and calculating the J(0) (or F_R2 or F_eta) values for each spin. The second >> step, performed outside relax, is the comparison of the calculated values at >> two magnetic fields (e.g. using correlation plots). >> >> It is important that data (all of R1, R2, and NOE) from a single magnetic >> field are loaded in order to calculate the J(0) (or F_R2 or F_eta) values. >> >> In the best of world, someone could implement the calculation of the J(0) >> (or F_R2 or F_eta) values at different fields and subsequent plotting and >> consistency assessment all within relax and in a single step. That would be >> a real enhancement compared to the current situation... :) >> >> I hope this helps. >> >> Best, >> >> >> Sébastien >> >> >> On 13-03-28 8:07 PM, Edward d'Auvergne wrote: >>> >>> Hi again, >>> >>> I was wondering if you have read the consistency testing part of the >>> relax manual written by Sebastien Morin (the person who implemented >>> this analysis). Specifically this section: >>> >>> >>> http://www.nmr-relax.com/manual/Consistency_testing_script_mode_relaxation_data_lo.html >>> >>> Note the text, "For this analysis, only data for a single field >>> strength can be loaded". This may possibly be the source of some of >>> your problems. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 28 March 2013 20:02, Edward d'Auvergne <[email protected]> wrote: >>>> >>>> Hi Mengjun, >>>> >>>> Could you also attach the PDB file? I need it to be able to run the >>>> script and replicate the problem. >>>> >>>> Cheers, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 28 March 2013 16:39, anonymous <[email protected]> >>>> wrote: >>>>> >>>>> Additional Item Attachment, bug #20674 (project relax): >>>>> >>>>> File name: T1 dhp 700.txt Size:74 KB >>>>> File name: T2 dhp 500.txt Size:67 KB >>>>> File name: T2 dhp 700.txt Size:68 KB >>>>> File name: logconsistency Size:371 KB >>>>> >>>>> >>>>> _______________________________________________________ >>>>> >>>>> Reply to this item at: >>>>> >>>>> <http://gna.org/bugs/?20674> >>>>> >>>>> _______________________________________________ >>>>> Message sent via/by Gna! >>>>> http://gna.org/ >>>>> >>>>> >>>>> _______________________________________________ >>>>> relax (http://www.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 >>> >>> >> >> -- >> Sébastien Morin, Ph.D. >> 1183 Bursins, Switzerland >> ---- sebastianomorino AT gmail.com ---- >> >> >> > > > > > _______________________________________________ > relax (http://www.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://www.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
