r20005 - /branches/relax_disp/user_functions/relax_disp.py -- June 10, 2013 - 14:10

Author: bugman
Date: Mon Jun 10 14:10:01 2013
New Revision: 20005

URL: http://svn.gna.org/viewcvs/relax?rev=20005&view=rev
Log:
Added the 'IT99' model to the relax_disp.select_model user function frontend.

This is the Ishima and Torchia 1999 2-site model for all timescales with pA 
> > pB.

This commit follows step 2 of the relaxation dispersion model addition 
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).


Modified:
    branches/relax_disp/user_functions/relax_disp.py

Modified: branches/relax_disp/user_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=20005&r1=20004&r2=20005&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Mon Jun 10 14:10:01 2013
@@ -39,7 +39,7 @@
 from specific_analyses.relax_disp.disp_data import cpmg_frq, relax_time, 
spin_lock_field
 from specific_analyses.relax_disp.nessy import nessy_input
 from specific_analyses.relax_disp.sherekhan import sherekhan_input
-from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_DPL94, 
MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_R2EFF
+from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_DPL94, 
MODEL_IT99, MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_R2EFF
 from specific_analyses.setup import relax_disp_obj
 from user_functions.data import Uf_info; uf_info = Uf_info()
 from user_functions.objects import Desc_container
@@ -440,6 +440,7 @@
         "%s: {R20, ...}" % MODEL_NOREX,
         "%s: {R20, ..., phi_ex, kex}" % MODEL_LM63,
         "%s: {R20, ..., pA, dw, kex}" % MODEL_CR72,
+        "%s: {R20, ..., phi_ex, padw2, kex}" % MODEL_IT99,
         "%s: {R1rho', ..., phi_ex, kex}" % MODEL_M61,
         "%s: {R1rho', ..., phi_ex, kex}" % MODEL_DPL94,
         "%s: {R1rho', ..., pA, dw, kex}" % MODEL_M61B
@@ -449,6 +450,7 @@
         MODEL_NOREX,
         MODEL_LM63,
         MODEL_CR72,
+        MODEL_IT99,
         MODEL_M61,
         MODEL_DPL94,
         MODEL_M61B
@@ -462,6 +464,7 @@
 uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX, "This is the model 
for no chemical exchange being present,")
 uf.desc[-1].add_item_list_element("'%s'" % MODEL_LM63, "The original Luz and 
Meiboom (1963) 2-site fast exchange equation with parameters {R20, phi_ex, 
kex},")
 uf.desc[-1].add_item_list_element("'%s'" % MODEL_CR72, "The Carver and 
Richards (1972) 2-site equation for all time scales with parameters {R2A, kA, 
dw}.")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_IT99, "The Ishima and 
Torchia (1999) 2-site model for all time scales with pA >> pB and with 
parameters {R20, phi_ex, padw2, kex}.")
 uf.desc[-1].add_paragraph("For the R1rho-type experiment, the currently 
supported models are:")
 uf.desc[-1].add_item_list_element("'%s'" % MODEL_R2EFF, "This is the same 
model model as for the CPMG-type experiments except that the R1rho and not 
R2eff values are determined.")
 uf.desc[-1].add_item_list_element("'%s'" % MODEL_NOREX, "This is the model 
for no chemical exchange being present,")
@@ -548,6 +551,20 @@
 
     zeta = -2delta_omega (pA.kex - pB.kex).\
 """)
+# IT99 model.
+uf.desc.append(Desc_container("The IT99 2-site CPMG model"))
+uf.desc[-1].add_paragraph("This is the model for 2-site exchange on all 
times scales (with the constraint that pA >> pB), named after Ishima and 
Torchia 1999.  Is it selected by setting the model to '%s'.  The equation 
is:" % MODEL_IT99)
+uf.desc[-1].add_verbatim("""\
+              phi_ex * tex
+    Rex ~= ------------------- ,
+           1 + omega_a^2*tex^2
+
+    phi_ex = pA * pB * delta_omega^2 ,
+    
+    omega_a^2 = sqrt(omega_1^4 + pB^2*delta_omega^2)\
+""")
+uf.desc[-1].add_paragraph("The reference for this equation is:")
+uf.desc[-1].add_list_element("Ishima R. and Torchia D.A. (1999).  Estimating 
the time scale of chemical exchange of proteins from measurements of 
transverse relaxation rates in solution.  J. Biomol. NMR, 14, 369-372.  (DOI: 
10.1023/A:1008324025406).")
 # M61 model.
 uf.desc.append(Desc_container("The M61 2-site fast exchange R1rho model"))
 uf.desc[-1].add_paragraph("This is the model for 2-site fast exchange for 
R1rho-type experiments.  It is selected by setting the model to '%s', here 
named after Meiboom 1961.  The equation for the exchange process is:" % 
MODEL_M61)