Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-19 Thread Sebastien Morin
Hi, I'll do the patch right away. Sorry for the attachment, I'll put a link next time... Cheers Séb Edward d'Auvergne wrote: > Hi, > > In this IUPAC report, on page 11, the radian unit is described as "The > units radian (rad) and steradian (sr), for plane angle and solid angle > respectivel

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-19 Thread Edward d'Auvergne
Hi, In this IUPAC report, on page 11, the radian unit is described as "The units radian (rad) and steradian (sr), for plane angle and solid angle respectively, are described as 'SI supplementary units' [3]. Since they are of dimension 1 (i.e. dimensionless), they may be included if appropriate, or

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-19 Thread Edward d'Auvergne
Hi, I have thoroughly checked all the units of the physical constants, spectral densities, rotational correlation times, and relaxation rates and have a few important corrections about the units which are used in relax and elsewhere. Please read below for the details and a long story about SI vs.

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-15 Thread Sebastien Morin
Hi, After a couple of chat with Leo Spyracopoulos, I understand better the link between s / rad ans s in spectral density mapping. Leo started with : "The results from the notebook should not be multiplied by 2 pi. Finally, by definition, a radian is a dimensionless quantity with no physical uni

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-15 Thread Sebastien Morin
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 i

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-15 Thread Sebastien Morin
Hi, Here are the different values I obtain for a residue with R1 = 1.1336 +- 0.0851 ; R2 = 12.9336 +- 0.9649 ; and NOE = 0.463921 +- 0.045 J(0) J(wN)J(wH) = == Here are the resul

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-15 Thread Edward d'Auvergne
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

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-13 Thread Sebastien Morin
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 fre

Re: [bug #9259] Reduced spectral density mapping yielding bad values

2007-06-01 Thread Edward d'Auvergne
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)