Hi, In an attempt to find the problem causing this bug, I dug into the code and found something which could be erroneous... This alone does not fix the bug, but may be part of the fix (or not)...
In function math_fns/direction_cosine.calc_ellipsoid_di(), there could be an error at line 229: diff_data.dz[1] = data.sin_b * data.sin_g If I am right (?), this part of the code is related to page 193 of Edward d'Auvergne's thesis: c11 = diff_data.dx[0] c21 = diff_data.dx[1] c31 = diff_data.dx[2] c12 = diff_data.dy[0] c22 = diff_data.dy[1] c32 = diff_data.dy[2] c13 = diff_data.dz[0] c23 = diff_data.dz[1] --> FALSE !!!! c33 = diff_data.dz[2] Indeed, c23 = sin(beta) * cos(gamma), whereas diff_data.dz[1] = data.sin_b * data.sin_g Thus, either me, the code or Edward's thesis are erroneous here... Am I right ? Regards, Séb :) Sébastien Morin wrote: > Hi, > > We (Pierre-Yves Savard and I) have found a problem with the > structure.create_diff_tensor_pdb() function. > > If you use either results.read() or diffusion_tensor.init() to load a > diffusion tensor and, then, display it, it is fine, except for the ellipsoid > where some weird things happen... > > Indeed, with the ellipsoid, you get a weird shaped tensor, depending on the > angles input. With angles set to 0, the tensor is fine. With alpha and beta > set to non-zero values, the shape of the tensor changes drastically as it > becomes completely flat. With gamma set to a non-zero value, the shape is > fine, with the tensor just turned around the Dz axis... > > I submitted a bug report and attached 7 files: > > tensor.pdb > With all angles set to 0. > > tensor__angles__alpha_90.pdb > With alpha = 90 degrees. > > tensor__angles__beta_90.pdb > With beta = 90 degrees. > > tensor__angles__gamma_90.pdb > With gamma = 90 degrees. > > tensor__angles__all_90.pdb > With all angles set to 90 degrees. > > tensor__angles__all_45.pdb > With all angles set to 45 degrees. > > tensor__angles__45_0_45.pdb > With all angles set to 45, 0 and 45 (alpha, beta and gamma, respectively). > > > As you will see, the tensor is fine if both alpha and beta are equal (files: > tensor__angles__all_45.pdb and tensor__angles__all_90.pdb), but weird shaped > when alpha and beta are not equal (tensor__angles__45_0_45.pdb)... > > These observations were made with the subversion repository. I verified with > relax-1.3.1 / relax-1.3.2 / relax-1.3.3 and the same problem arises... so the > problem as been there for a long time... > > Shouldn't the tensor always keep a symmetric shape, with angles only changing > the orientation, not the shape..? > > Thanks for help. > > > Séb :) > -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université Laval > & PROTEO Québec, Canada > > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > relax-users@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-users > -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université Laval & PROTEO Québec, Canada _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@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-users