URL: <http://gna.org/bugs/?13032> Summary: Bug in structure.create diff tensor pdb Project: relax Submitted by: semor Submitted on: Friday 02/20/2009 at 08:45 Category: relax's source code Severity: 3 - Normal Priority: 5 - Normal Status: None Privacy: Public Assigned to: None Originator Name: Originator Email: Open/Closed: Open Discussion Lock: Any Release: Repository: 1.3 line Operating System: GNU/Linux _______________________________________________________ Details: 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 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. _______________________________________________________ File Attachments: ------------------------------------------------------- Date: Friday 02/20/2009 at 08:45 Name: tensor.pdb Size: 36kB By: semor <http://gna.org/bugs/download.php?file_id=5323> ------------------------------------------------------- Date: Friday 02/20/2009 at 08:45 Name: tensor__angles__alpha_90.pdb Size: 36kB By: semor <http://gna.org/bugs/download.php?file_id=5324> ------------------------------------------------------- Date: Friday 02/20/2009 at 08:45 Name: tensor__angles__all_90.pdb Size: 36kB By: semor <http://gna.org/bugs/download.php?file_id=5325> ------------------------------------------------------- Date: Friday 02/20/2009 at 08:45 Name: tensor__angles__beta_90.pdb Size: 36kB By: semor <http://gna.org/bugs/download.php?file_id=5326> _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?13032> _______________________________________________ Message sent via/by Gna! http://gna.org/