r2692 - /branches/tensor_pdb/prompt/pdb.py -- October 29, 2006 - 05:55

Author: bugman
Date: Sun Oct 29 05:54:29 2006
New Revision: 2692

URL: http://svn.gna.org/viewcvs/relax?rev=2692&view=rev
Log:
Improved the docstring of the user function 'pdb.create_tensor_pdb()'.

I've made it more clear that the units of the diffusion tensor are rates, not 
times.  This is to
help users to not be confused with the fact that being parallel to the long 
axis of the tensor means
that the bond is moving faster!


Modified:
    branches/tensor_pdb/prompt/pdb.py

Modified: branches/tensor_pdb/prompt/pdb.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/pdb.py?rev=2692&r1=2691&r2=2692&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/pdb.py (original)
+++ branches/tensor_pdb/prompt/pdb.py Sun Oct 29 05:54:29 2006
@@ -58,17 +58,18 @@
         Description
         ~~~~~~~~~~~
 
-        This function creates a PDB file containing artificial structures 
which represent the
-        diffusion tensor.  A structure must have previously been read.  The 
diffusion tensor is
-        represented by an ellipsoidal, spheroidal, or spherical geometric 
object with its origin
-        located at the center of mass.  This diffusion tensor PDB file can 
subsequently read into
-        any molecular viewer.
-
-        As the units of the Brownian rotational diffusion tensor is the rate 
of diffusion measured
-        in inverse seconds, the size of the tensor geometric object is hence 
proportional to the
-        rate and not the correlation times.  Hence the larger the geometric 
object, the faster the
-        diffusion of a molecule.  For example the diffusion tensor of a 
water molecule is much
-        larger than the diffusion tensor of a macromolecule.
+        IMPORTANT:  As the units of the Brownian rotational diffusion tensor 
is the rate of
+        diffusion measured in inverse seconds, the size of the tensor 
geometric object is hence
+        proportional to the rate and is not a correlation time.  Hence the 
larger the geometric
+        object, the faster the diffusion of a molecule.  For example the 
diffusion tensor of a water
+        molecule is much larger than the diffusion tensor of a 
macromolecule.  Hence, XH bond
+        vectors parallel to the longest axis of the tensor tumble the 
fastest. 
+
+        This function creates a PDB file containing an artificial geometric 
structure to represent
+        the diffusion tensor.  A structure must have previously been read 
into relax.  The diffusion
+        tensor is represented by an ellipsoidal, spheroidal, or spherical 
geometric object with its
+        origin located at the center of mass (of the selected residues).  
This diffusion tensor PDB
+        file can subsequently read into any molecular viewer.
 
         The scaling argument can be used to vary the size of the tensor 
geometric object.  The
         default value is 1.8e-6.  For spherical diffusion with a global 
correlation time of 10 ns