Re: [bug #9259] Reduced spectral density mapping yielding bad values
Hi, That is awesome work tracking down this problem. Thank you! I'll apply your patch and then hopefully make a new relax 1.2 release with your fixes very soon. I do have a important question first though. My question relates to the multiplication of the frequency by 2pi to convert from Hz to rad/s units. The symbol for the frequency in Hz is nu whereas the frequency in rad/s is omega. In all the relaxation equations composed of spectral density components, the frequencies are in rad/s and are represented by the omega symbol. This includes the CSA constant defined in SI units as c = (omegaX.CSA)^2/3, where CSA is the chemical shift anisotropy and omegaX = gammaX.B0. To get nuX which is the frequency of the X nucleus in Hz, omegaX measured in rad/s should be divided by 2pi. So my question is, do you get the same results as the Mathematica notebooks of Leo Spyracopoulos if you retain the multiplication of the frequency by 2pi? Thanks, Edward P.S. The problem with the list of frequencies is probably the major issue. I'm not sure why I attempted to fill out the entire list of frequencies as the reduced spectral density mapping code only uses the value in self.data.frq_list[0, 1], the frequency of the heteronucleus, to calculate the CSA constant. The higher frequencies are never used in the calculation. Anyway, your patch fixes this problem. On 6/13/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi ! I've checked the equations used for reduced spectral density mapping in relax. They're all right... The assumption about the factor of (mu0 / (4pi))^2 is ok since the old equations were written in Gaussian units (cgs) and now we use SI units. However, 2 things seem to be wrong. 1. The frequencies need not to be scaled by a factor of 2 pi since the unit of frequency in the SI is Hz. Thus, line 52 of 'maths_fns/jw_mapping.py' must be removed. 2. The frequency used for calculating the CSA seems not to be the heteronuclear frequency. In fact, there is an error in lines 57 to 60 from 'maths_fns/jw_mapping.py' since the same item in the list is assigned different values one after the other. Changing those lines from : self.data.frq_list[0, 1] = frqX self.data.frq_list[0, 1] = frq - frqX self.data.frq_list[0, 1] = frq self.data.frq_list[0, 1] = frq + frqX to : self.data.frq_list[0, 1] = frqX self.data.frq_list[0, 2] = frq - frqX self.data.frq_list[0, 3] = frq self.data.frq_list[0, 4] = frq + frqX should work. The important thing is that item 1 stays the heteronuclear frequency so it matches with line 1020 of 'maths_fns/ri_comps.py' : data.csa_const_fixed[j] = data.frq_sqrd_list[j, 1] / 3.0 where the constant 'c' is calculated using the squared heteronuclear frequency. With those two modifications, I now get the same values as when calculating manually or using Leo Spyracopoulos's Mathematica notebooks (http://www.bionmr.ualberta.ca/~lspy/index_7.html). Bye ! Sébastien :) Edward d'Auvergne wrote: 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 [EMAIL PROTECTED] 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 -
[bug #9259] Reduced spectral density mapping yielding bad values
Additional Item Attachment, bug #9259 (project relax): File name: patch_2007-06-15 Size:0 KB ___ 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@gna.org 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
Re: [bug #9259] Reduced spectral density mapping yielding bad values
Hi, I made a patch for the test-suite so the spectral density test passes (patch_2007-06-15)... This patch should go with the one for solving the bug that I uploaded yesterday. Cheers Sébastien P.S. I have a question about the test-suite. Should the test-suite files be modified when a patch is sent as an answer to a bug report ? The patch from yesterday made the test-suite fail, I believe it is thus fine to also make a patch for the test-suite. Do you prefer making 2 different patches or a single one with everything in it (as the output from svn diff) ? Edward d'Auvergne wrote: Hi, That is awesome work tracking down this problem. Thank you! I'll apply your patch and then hopefully make a new relax 1.2 release with your fixes very soon. I do have a important question first though. My question relates to the multiplication of the frequency by 2pi to convert from Hz to rad/s units. The symbol for the frequency in Hz is nu whereas the frequency in rad/s is omega. In all the relaxation equations composed of spectral density components, the frequencies are in rad/s and are represented by the omega symbol. This includes the CSA constant defined in SI units as c = (omegaX.CSA)^2/3, where CSA is the chemical shift anisotropy and omegaX = gammaX.B0. To get nuX which is the frequency of the X nucleus in Hz, omegaX measured in rad/s should be divided by 2pi. So my question is, do you get the same results as the Mathematica notebooks of Leo Spyracopoulos if you retain the multiplication of the frequency by 2pi? Thanks, Edward P.S. The problem with the list of frequencies is probably the major issue. I'm not sure why I attempted to fill out the entire list of frequencies as the reduced spectral density mapping code only uses the value in self.data.frq_list[0, 1], the frequency of the heteronucleus, to calculate the CSA constant. The higher frequencies are never used in the calculation. Anyway, your patch fixes this problem. On 6/13/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi ! I've checked the equations used for reduced spectral density mapping in relax. They're all right... The assumption about the factor of (mu0 / (4pi))^2 is ok since the old equations were written in Gaussian units (cgs) and now we use SI units. However, 2 things seem to be wrong. 1. The frequencies need not to be scaled by a factor of 2 pi since the unit of frequency in the SI is Hz. Thus, line 52 of 'maths_fns/jw_mapping.py' must be removed. 2. The frequency used for calculating the CSA seems not to be the heteronuclear frequency. In fact, there is an error in lines 57 to 60 from 'maths_fns/jw_mapping.py' since the same item in the list is assigned different values one after the other. Changing those lines from : self.data.frq_list[0, 1] = frqX self.data.frq_list[0, 1] = frq - frqX self.data.frq_list[0, 1] = frq self.data.frq_list[0, 1] = frq + frqX to : self.data.frq_list[0, 1] = frqX self.data.frq_list[0, 2] = frq - frqX self.data.frq_list[0, 3] = frq self.data.frq_list[0, 4] = frq + frqX should work. The important thing is that item 1 stays the heteronuclear frequency so it matches with line 1020 of 'maths_fns/ri_comps.py' : data.csa_const_fixed[j] = data.frq_sqrd_list[j, 1] / 3.0 where the constant 'c' is calculated using the squared heteronuclear frequency. With those two modifications, I now get the same values as when calculating manually or using Leo Spyracopoulos's Mathematica notebooks (http://www.bionmr.ualberta.ca/~lspy/index_7.html). Bye ! Sébastien :) Edward d'Auvergne wrote: 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
