r22918 - /trunk/lib/dispersion/b14.py -- May 02, 2014 - 11:57

Author: tlinnet
Date: Fri May  2 11:57:07 2014
New Revision: 22918

URL: http://svn.gna.org/viewcvs/relax?rev=22918&view=rev
Log:
Python API documentation corrections for the model B14.

sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014) 
B14 model - 2-site exact solution model for all time scales.

"This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list";

The B14 model is explained in: http://wiki.nmr-relax.com/B14.

Modified:
    trunk/lib/dispersion/b14.py

Modified: trunk/lib/dispersion/b14.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=22918&r1=22917&r2=22918&view=diff
==============================================================================
--- trunk/lib/dispersion/b14.py (original)
+++ trunk/lib/dispersion/b14.py Fri May  2 11:57:07 2014
@@ -41,6 +41,7 @@
 =========
 
 The equation used is::
+
             R2A0 + R2B0 + kex      Ncyc                      1      ( 1+y    
        1-y                          )
     R2eff = ------------------ -  ------ * cosh^-1 * v1c - ------ ln( --- + 
------------------ * (v2 + 2*kAB*pD ) )   
                   2                Trel                     Trel    (  2    
2*sqrt(v1c^2 -1 )                     )
@@ -50,6 +51,7 @@
                            Trel    (  2    2*sqrt(v1c^2 -1 )                 
    )
 
 Which have these following definitions::
+
     v1c = F0 * cosh(tauCP * E0)- F2 * cosh(tauCP * E2) 
     v1s = F0 * sinh(tauCP * E0)- F2 * sinh(tauCP * E2) 
     v2*N = v1s * (OB-OA) + 4OB * F1^a * sinh(tauCP * E1) 
@@ -57,23 +59,20 @@
     v3 = ( v2^2 + 4 * kBA * kAB * pD^2 )^1/2 
     y = ( (v1c-v3)/(v1c+v3) )^NCYC
 
-Note, E2 is complex. If |x| denotes the complex modulus:<br>
+Note, E2 is complex. If |x| denotes the complex modulus::
+
     cosh(tauCP * E2) = cos(tauCP * |E2|)
     sinh(tauCP * E2) = i sin(tauCP * |E2|)
 
 The term pD is based on product of the off diagonal elements in the CPMG 
propagator (Supplementary Section 3).
 
-It is interesting to consider the region of validity of the Carver Richards 
result.
-The two results are equal when the correction is zero, which is true when
+It is interesting to consider the region of validity of the Carver Richards 
result.  The two results are equal when the correction is zero, which is true 
when::
 
     sqrt(v1c^2-1) ~ v2 + 2*kAB * pD
 
-This occurs when 2*kAB * pD tends to zero, and so v2=v3.
-Setting "kAB * pD" to zero, amounts to neglecting magnetisation that starts 
on the ground state ensemble and end on the excited state ensemble and vice 
versa.
-This will be a good approximation when pA >> p_B.
+This occurs when 2*kAB * pD tends to zero, and so v2=v3.  Setting "kAB * pD" 
to zero, amounts to neglecting magnetisation that starts on the ground state 
ensemble and end on the excited state ensemble and vice versa.  This will be 
a good approximation when pA >> p_B.
 
-In practise, significant deviations from the Carver Richards equation can be 
incurred if pB > 1 %.
-Incorporation of the correction term into equation (50), results in an 
improved description of the CPMG experiment over the Carver Richards equation.
+In practise, significant deviations from the Carver Richards equation can be 
incurred if pB > 1 %.  Incorporation of the correction term into equation 
(50), results in an improved description of the CPMG experiment over the 
Carver Richards equation.
 
 kex is the chemical exchange rate constant, pA and pB are the populations of 
states A and B, and delta_omega is the chemical shift difference between the 
two states in ppm.