Author: bugman
Date: Sun Jun 9 22:18:38 2013
New Revision: 19998
URL: http://svn.gna.org/viewcvs/relax?rev=19998&view=rev
Log:
Added the 'DPL94' model to the relax_disp.select_model user function frontend.
This is the David, Perlman and London 1994 R1rho 2-site fast exchange model.
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=19998&r1=19997&r2=19998&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Sun Jun 9 22:18:38 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_LM63,
MODEL_M61, MODEL_M61B, MODEL_NOREX, MODEL_R2EFF
+from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_DPL94,
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
@@ -441,6 +441,7 @@
"%s: {R20, ..., phi_ex, kex}" % MODEL_LM63,
"%s: {R20, ..., pA, dw, kex}" % MODEL_CR72,
"%s: {R1rho', ..., phi_ex, kex}" % MODEL_M61,
+ "%s: {R1rho', ..., phi_ex, kex}" % MODEL_DPL94,
"%s: {R1rho', ..., pA, dw, kex}" % MODEL_M61B
],
wiz_combo_data = [
@@ -449,6 +450,7 @@
MODEL_LM63,
MODEL_CR72,
MODEL_M61,
+ MODEL_DPL94,
MODEL_M61B
],
wiz_read_only = True
@@ -464,6 +466,7 @@
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,")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_M61, "The Meiboom (1961)
2-site fast exchange equation with parameters {R1rho', phi_ex, kex},")
+uf.desc[-1].add_item_list_element("'%s'" % MODEL_DPL94, "The Davis, Perlman
and London (1994) 2-site fast exchange equation with parameters {R1rho',
phi_ex, kex},")
uf.desc[-1].add_item_list_element("'%s'" % MODEL_M61B, "The Meiboom (1961)
2-site equation for all time scales with parameters {R1rho', pA, dw, kex},")
uf.desc[-1].add_paragraph("Except for '%s', these CPMG and R1rho models are
fit to clusterings of spins, or spin blocks. The models are described in
more detail below." % MODEL_R2EFF)
# R2eff model.
@@ -560,6 +563,25 @@
uf.desc[-1].add_paragraph("kex is the chemical exchange rate constant, pA
and pB are the populations of states A and B, delta_omega is the chemical
shift difference between the two states, and omega_e is the effective field
in the rotating frame.")
uf.desc[-1].add_paragraph("The reference for this equation is:")
uf.desc[-1].add_list_element("Meiboom S. (1961). Nuclear magnetic resonance
study of the proton transfer in water. J. Chem. Phys., 34, 375-388. (DOI:
10.1063/1.1700960).")
+# DPL94 model.
+uf.desc.append(Desc_container("The DPL94 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_DPL94)
+uf.desc[-1].add_verbatim("""\
+ phi_ex * kex
+ R1rho = R1rho' + sin^2(theta) * ----------------- ,
+ kex^2 + omega_e^2\
+""")
+uf.desc[-1].add_paragraph("where R1rho' is the R1rho value in the absence of
exchange equal to")
+uf.desc[-1].add_verbatim("""\
+ R1rho' = R1.cos^2(theta) + R2.sin^2(theta) ,\
+""")
+uf.desc[-1].add_paragraph("theta is the rotating frame tilt angle,")
+uf.desc[-1].add_verbatim("""\
+ phi_ex = pA * pB * delta_omega^2 ,\
+""")
+uf.desc[-1].add_paragraph("kex is the chemical exchange rate constant, pA
and pB are the populations of states A and B, delta_omega is the chemical
shift difference between the two states, and omega_e is the effective field
in the rotating frame.")
+uf.desc[-1].add_paragraph("The reference for this equation is:")
+uf.desc[-1].add_list_element("Davis, D. G., Perlman, M. E. and London, R. E.
(1994). Direct measurements of the dissociation-rate constant for
inhibitor-enzyme complexes via the T1rho and T2 (CPMG) methods. J. Magn.
Reson, Series B, 104, 266-275. (DOI: 10.1006/jmrb.1994.1084).")
# M61 skew model.
uf.desc.append(Desc_container("The M61 2-site, skewed, on-resonance R1rho
model"))
uf.desc[-1].add_paragraph("This is the Meiboom 1961 model for 2-site
exchange on all time scales for R1rho-type experiments. It only holds for
on-resonance experiments and when the populations are significantly skewed
(pA >> pB). It is selected by setting the model to '%s'. The equation for
the exchange process is:" % MODEL_M61B)
r19998 - /branches/relax_disp/user_functions/relax_disp.py