r2689 - in /branches/tensor_pdb: data.py generic_fns/pdb.py -- October 29, 2006 - 04:14

Author: bugman
Date: Sun Oct 29 04:13:38 2006
New Revision: 2689

URL: http://svn.gna.org/viewcvs/relax?rev=2689&view=rev
Log:
Fixed the transposed spheroidal rotation matrix.

The spheroidal rotation matrix returned from the data structure 
'self.relax.data.diff[run].rotation'
was incorrect.  Instead of the true rotation matrix, the transpose of the 
matrix was being returned.
As the spheroidal rotation matrix was transposed whereas the ellipsoidal 
rotation matrix was correct
(the spherical rotation matrix was the identity matrix, so no problem there), 
the maths for
generating the PDB geometric object representing the diffusion tensor was 
causing problems.  Now all
three geometric objects - sphere, spheroid, and ellipsoid - should be 
correctly generated.


Modified:
    branches/tensor_pdb/data.py
    branches/tensor_pdb/generic_fns/pdb.py

Modified: branches/tensor_pdb/data.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/data.py?rev=2689&r1=2688&r2=2689&view=diff
==============================================================================
--- branches/tensor_pdb/data.py (original)
+++ branches/tensor_pdb/data.py Sun Oct 29 04:13:38 2006
@@ -217,9 +217,9 @@
         The rotation matrix required to shift from the diffusion tensor 
frame to the PDB frame is
         equal to
 
-                  |  cos(theta) * cos(phi)   cos(theta) * sin(phi)  
-sin(theta) |
-            R  =  | -sin(phi)                cos(phi)                0       
   |.
-                  |  sin(theta) * cos(phi)   sin(theta) * sin(phi)   
cos(tehta) |
+                  |  cos(theta) * cos(phi)  -sin(phi)   sin(theta) * 
cos(phi) |
+            R  =  |  cos(theta) * sin(phi)   cos(phi)   sin(theta) * 
sin(phi) |.
+                  | -sin(theta)              0          cos(theta)           
 |
 
 
         Ellipsoidal diffusion
@@ -262,9 +262,9 @@
 
             R  =  | Dx_unit  Dy_unit  Dz_unit |,
 
-                  | Dx_unit[0]  Dy_unit[0]  Dz_unit[0] | 
+                  | Dx_unit[0]  Dy_unit[0]  Dz_unit[0] |
                =  | Dx_unit[1]  Dy_unit[1]  Dz_unit[1] |.
-                  | Dx_unit[2]  Dy_unit[2]  Dz_unit[2] | 
+                  | Dx_unit[2]  Dy_unit[2]  Dz_unit[2] |
         """
 
         # All tensor types.
@@ -339,9 +339,9 @@
 
         # The diffusion tensor (within the structural frame).
         if name == 'tensor' and self.type == 'spheroid':
-            # Rotation (R^T . tensor . R).
+            # Rotation (R . tensor . R^T).
             R = self.rotation
-            return dot(transpose(R), dot(self.tensor_diag, R))
+            return dot(R, dot(self.tensor_diag, transpose(R)))
 
         # The rotation matrix.
         if name == 'rotation' and self.type == 'spheroid':
@@ -350,15 +350,15 @@
 
             # First row of the rotation matrix.
             rotation[0, 0] = cos(self.theta) * cos(self.phi)
-            rotation[0, 1] = cos(self.theta) * sin(self.phi)
-            rotation[0, 2] = -sin(self.theta)
+            rotation[1, 0] = cos(self.theta) * sin(self.phi)
+            rotation[2, 0] = -sin(self.theta)
 
             # Second row of the rotation matrix.
-            rotation[1, 0] = -sin(self.phi)
+            rotation[0, 1] = -sin(self.phi)
             rotation[1, 1] = cos(self.phi)
 
             # Replace the last row of the rotation matrix with the Dpar unit 
vector.
-            rotation[2] = self.Dpar_unit
+            rotation[:, 2] = self.Dpar_unit
 
             # Return the tensor.
             return rotation

Modified: branches/tensor_pdb/generic_fns/pdb.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2689&r1=2688&r2=2689&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 04:13:38 2006
@@ -21,7 +21,7 @@
 
###############################################################################
 
 from math import sqrt, cos, pi, sin
-from Numeric import Float64, arccos, dot, transpose, zeros
+from Numeric import Float64, arccos, dot, zeros
 from os import F_OK, access
 from re import compile
 import Scientific.IO.PDB
@@ -309,7 +309,7 @@
         ######################
 
         # Print out.
-        print "Creating the vector distribution."
+        print "Creating the vector distribution.\n"
 
         # Increment value.
         inc = 20
@@ -328,7 +328,7 @@
                 atom_id = 'T' + `i` + 'P' + `j`
 
                 # Rotate the vector into the diffusion frame.
-                vector = 
dot(transpose(self.relax.data.diff[self.run].rotation), vectors[index])
+                vector = dot(self.relax.data.diff[self.run].rotation, 
vectors[index])
 
                 # Set the length of the vector to its diffusion rate within 
the diffusion tensor geometric object.
                 vector = dot(self.relax.data.diff[self.run].tensor, vector)