Hi, For the reduced spectral density mapping in relax, I have used equations 10 to 12 from: Markus M. A., Dayie K. T., Matsudaira P., and Wagner G. Local mobility within villin 14T probed via heteronuclear relaxation measurements and a reduced spectral density mapping. Biochemistry. 1996, 35(6):1722-32. The equations themselves are derived from: Lefevre J. F., Dayie K. T., Peng J. W., and Wagner G. Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions. Biochemistry. 1996, 35(8):2674-86. One problem may be that I made the assumption that the dipolar constant of equation 7 of the first reference was missing the factor of (mu0 / (4pi))^2! I based this assumption on the SI units formulation of the R1, R2, and NOE equations and how the CSA constant is defined. I think this is a fairly safe assumption though if you look at equations 1, 2, and 8 of that paper. Could the problem be the definition of the equations used? I've looked at the code in relax and it seems to replicate these equations correctly. Are the equations of Markus et al., (1996) correct? Is my assumption about the dipolar constant correct? If you manually calculate the reduced spectral density values using these alternative equations, does relax produce the same values? I'm sorry that I can't exactly pinpoint the problem, but something is seriously amiss. Regards, Edward On 6/1/07, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL: <http://gna.org/bugs/?9259> Summary: Reduced spectral density mapping yielding bad values Project: relax Submitted by: None Submitted on: Friday 06/01/2007 at 17:15 CEST Category: relax's source code Severity: 4 - Important Priority: 5 - Normal Status: None Privacy: Public Assigned to: None Originator Name: Sébastien Morin Originator Email: sebastien.morin.1@xxxxxxxxx Open/Closed: Open Discussion Lock: Any Release: Repository: 1.2 line Operating System: GNU/Linux _______________________________________________________ Details: Hi I performed spectral density mapping on data recorded at three magnetic fields (500, 600, 800). The values I get are erroneous (when compared with Leo Spyracopoulos' Mathematica notebook which were manually verified using equations from the method 1 of Farrow et al., 1995, JBNMR, 6 : 153) and scaled depending on the magnetic field as shown in the table below (for which values calculated using either Leo's notebook or relax are divided by the value calculated manually). Field Method J(0) J(wN) J(wH) ===== ======= ========== ========== ========== 500 Farrow 1 (ref) 1 (ref) 1 (ref) Leo 1 1 1 relax 0.04758 0.04757 0.999 600 Farrow 1 (ref) 1 (ref) 1 (ref) Leo 1 1 1 relax 0.03361 0.03361 0.999 800 Farrow 1 (ref) 1 (ref) 1 Leo 1 1 1 relax 0.01932 0.01932 0.999 Then, if you take the different values for J(0) and J(wN) and compare from field to field, you get this : J(0) J(wN) J(wH) ======== ======== ======== 500/600 -> 1.415 1.415 1 500/800 -> 2.462 2.462 1 Those ratios are similar to what you get when comparing fields quadratically : (600/500)^2 = (1.2)^2 = 1.44 ~ 1.415 (800/500)^2 = (1.6)^2 = 2.56 ~ 2.462 So there seems to be a problem somewhere in the calculations of J(0) and J(wN) and, to a lesser extent, J(wH)... I first thought the problem was related with bug #9238... In fact, before this bug was solved, the problem was worst by a factor of ~2... Still, the skewing of Jw mapping results is quite important. Maybe is this something with the units or constants values... Thanks for helping me ! Sébastien :) _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?9259> _______________________________________________ Message sent via/by Gna! http://gna.org/ _______________________________________________ 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