Author: bugman
Date: Mon Jun 10 15:48:36 2013
New Revision: 20014
URL: http://svn.gna.org/viewcvs/relax?rev=20014&view=rev
Log:
Added the support for the tex parameter (tex = 1/(2kex)) to the dispersion
specific analysis.
This is needed for the Ishima and Torchia 1999 2-site model for all
timescales with pA >> pB.
This commit follows step 5 of the relaxation dispersion model addition
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=20014&r1=20013&r2=20014&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Mon Jun 10
15:48:36 2013
@@ -100,6 +100,7 @@
self.PARAMS.add('padw2', scope='spin', default=1.0, desc='The
pA.dw**2 value (ppm^2)', set='params', py_type=float,
grace_string='\\qp\\sA\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True,
sim=True)
self.PARAMS.add('dw', scope='spin', default=0.0, desc='The chemical
shift difference between states A and B (in ppm)', set='params',
py_type=float, grace_string='\\q\\xDw\f{}\\Q (ppm)', err=True, sim=True)
self.PARAMS.add('kex', scope='spin', default=10000.0, desc='The
exchange rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.add('tex', scope='spin', default=1.0/20000.0, desc='The
time of exchange (tex = 1/(2kex))', set='params', py_type=float,
grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('r2a', scope='spin', default=15.0, desc='The
transversal relaxation rate for state A', set='params', py_type=float,
grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('ka', scope='spin', default=10000.0, desc='The
exchange rate from state A to state B', set='params', py_type=float,
grace_string='\\qk\\sA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
self.PARAMS.add('params', scope='spin', desc='The model parameters',
py_type=list)
@@ -416,6 +417,11 @@
elif spin.params[i] in ['kex', 'ka']:
lower.append(1.0)
upper.append(100000.0)
+
+ # Time of exchange.
+ elif spin.params[i] in ['tex']:
+ lower.append(1/200000.0)
+ upper.append(0.5)
# The full grid size.
grid_size = 1
@@ -1584,6 +1590,7 @@
_table.add_row(["Chemical shift difference between states A and B
(ppm)", "'dw'"])
_table.add_row(["Exchange rate (rad/s)", "'kex'"])
_table.add_row(["Exchange rate from state A to state B (rad/s)", "'ka'"])
+ _table.add_row(["Time of exchange (s/rad)", "'tex'"])
_table.add_row(["Peak intensities (series)", "'intensities'"])
_table.add_row(["CPMG pulse train frequency (series, Hz)",
"'cpmg_frqs'"])
return_data_name_doc.add_table(_table.label)
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=20014&r1=20013&r2=20014&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Mon Jun 10
15:48:36 2013
@@ -156,6 +156,10 @@
elif param_name in ['kex', 'ka']:
scaling_matrix[param_index, param_index] = 10000
+ # Time of exchange scaling.
+ elif param_name == 'tex':
+ scaling_matrix[param_index, param_index] = 1e4
+
# Return the scaling matrix.
return scaling_matrix
@@ -257,6 +261,7 @@
padw2 >= 0
dw >= 0
kex >= 0
+ tex >= 0
kA >= 0
@@ -274,9 +279,9 @@
| 1 0 0 | | pA | | 0.5 |
| | | | | |
|-1 0 0 | | pA | | -1 |
+ | | | | | |
+ | 1 0 0 | | pA | | 0.85 |
| | . | | >= | |
- | 1 0 0 | | pA | | 0.85 |
- | | | | | |
| 1 0 0 | | phi_ex | | 0 |
| | | | | |
| 1 0 0 | | padw2 | | 0 |
@@ -284,6 +289,8 @@
| 1 0 0 | | dw | | 0 |
| | | | | |
| 1 0 0 | | kex | | 0 |
+ | | | | | |
+ | 1 0 0 | | tex | | 0 |
| | | | | |
| 1 0 0 | | kA | | 0 |
@@ -376,8 +383,8 @@
b.append(0.5 / scaling_matrix[param_index, param_index])
j += 1
- # Exchange rates (k >= 0).
- elif param_name in ['kex', 'ka']:
+ # Exchange rates and times (k >= 0 and t >= 0).
+ elif param_name in ['kex', 'ka', 'tex']:
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
b.append(0.0)
r20014 - in /branches/relax_disp/specific_analyses/relax_disp: __init__.py parameters.py