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
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Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada
Re: Bug in structure.create diff tensor pdb