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
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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>
_______________________________________________________
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<http://gna.org/bugs/?13032>
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[bug #13032] Bug in structure.create diff tensor pdb