Author: bugman
Date: Sat Sep 27 17:58:49 2014
New Revision: 26093
URL: http://svn.gna.org/viewcvs/relax?rev=26093&view=rev
Log:
Merged revisions 26085,26087-26088 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26085 | tlinnet | 2014-09-27 12:20:33 +0200 (Sat, 27 Sep 2014) | 12 lines
For relaxation dispersion, modified that the Grid search and linear
constraints for parameter "k_AB" is between 0-100.
The parameter is only used in the TSMFK01 model.
The "k_AB" parameter is only for very slow forward exchange rate.
The extected values should according to the reference paper:
Tollinger, M., Skrynnikov, N. R., Mulder, F. A. A., Forman-Kay, J. D., and
Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an sh3
domain. J. Am. Chem. Soc., 123(46), 11341-11352. (10.1021/ja011300z)
The paper conserns values of k_AB in the region 0.1 to 5.0.
If the exchange rate is any higher value of this, then another model should
be used for the analysis.
........
r26087 | tlinnet | 2014-09-27 14:49:46 +0200 (Sat, 27 Sep 2014) | 3 lines
Set the default insignificance value to 0.0 instead of 1.0.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
........
r26088 | tlinnet | 2014-09-27 16:33:01 +0200 (Sat, 27 Sep 2014) | 3 lines
Modified the Grid search limits for parameter "k_AB" to be between 0.1 and
20.0 rad/s.
This is for the TSMFK01 model, where values much above 10/20 is not
expected.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sat Sep 27 17:58:49 2014
@@ -1 +1 @@
-/trunk:1-26017,26043-26072
+/trunk:1-26092
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py?rev=26093&r1=26092&r2=26093&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
(original)
+++ branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
Sat Sep 27 17:58:49 2014
@@ -106,7 +106,7 @@
# The R2eff/R1rho value in rad/s by which to judge insignificance.
If the maximum difference between two points on all dispersion curves for a
spin is less than this value, that spin will be deselected.
if 'insignificance' not in self.settings:
- self.set_self(key='insignificance', value=1.0)
+ self.set_self(key='insignificance', value=0.0)
# A flag which if True will activate R1 parameter fitting via
relax_disp.r1_fit for the models that support it.
# If False, then the relax_disp.r1_fit user function will not be
called.
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py?rev=26093&r1=26092&r2=26093&view=diff
==============================================================================
---
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
(original)
+++
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
Sat Sep 27 17:58:49 2014
@@ -568,13 +568,13 @@
self._add(
'k_AB',
scope = 'spin',
- default = 1000.0,
+ default = 2.0,
desc = 'The exchange rate from state A to state B',
py_type = float,
set = 'params',
- scaling = 10000,
- grid_lower = 1.0,
- grid_upper = 10000.0,
+ scaling = 20,
+ grid_lower = 0.1,
+ grid_upper = 20.0,
grace_string = '\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)',
err = True,
sim = True
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py?rev=26093&r1=26092&r2=26093&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/relax_disp/parameters.py
Sat Sep 27 17:58:49 2014
@@ -446,11 +446,10 @@
padw2 >= 0
dw >= 0
0 <= kex <= 2e6
- 0 <= k_AB <= 2e6
0 <= kB <= 2e6
0 <= kC <= 2e6
+ 0 <= k_AB <= 100
tex >= 0
- k_AB >= 0
Matrix notation
@@ -504,9 +503,11 @@
| | | | | |
|-1 0 0 | | kC | | -2e6 |
| | | | | |
+ | 1 0 0 | | k_AB | | 0 |
+ | | | | | |
+ |-1 0 0 | | k_AB | | 100 |
+ | | | | | |
| 1 0 0 | | tex | | 0 |
- | | | | | |
- | 1 0 0 | | k_AB | | 0 |
@keyword spins: The list of spin data containers for the
block.
@@ -621,13 +622,23 @@
break
# Exchange rates and times (0 <= k <= 2e6).
- elif param_name in ['kex', 'kex_AB', 'kex_AC', 'kex_BC', 'k_AB',
'kB', 'kC']:
+ elif param_name in ['kex', 'kex_AB', 'kex_AC', 'kex_BC', 'kB', 'kC']:
A.append(zero_array * 0.0)
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
A[j+1][param_index] = -1.0
b.append(0.0)
b.append(-2e6 / scaling_matrix[param_index, param_index])
+ j += 2
+
+ # Exchange rates and times (0 <= k_AB <= 100).
+ elif param_name in ['k_AB']:
+ A.append(zero_array * 0.0)
+ A.append(zero_array * 0.0)
+ A[j][param_index] = 1.0
+ A[j+1][param_index] = -1.0
+ b.append(0.0)
+ b.append(-100. / scaling_matrix[param_index, param_index])
j += 2
# Exchange times (tex >= 0).
r26093 - in /branches/frame_order_cleanup: ./ auto_analyses/ specific_analyses/relax_disp/