Author: tlinnet
Date: Fri Aug 15 15:11:00 2014
New Revision: 25024
URL: http://svn.gna.org/viewcvs/relax?rev=25024&view=rev
Log:
Modified the Linear Constraints for the exchange rates.
For CPMG, the maximum kex should be 10^4, and for R1rho it should be 10^5.
This is altered from the value of 10^6.
The suggested restraints for 'kex' follows from article, on page 224:
Nuclear Magnetic Resonance Methods for Quantifying Microsecond-to-Millisecond
Motions in Biological Macromolecules.
Palmer-III, Arthur G., Kroenke, Christopher D., Loria, J. Patrick
Nucl. Magn. Reson. Biol. Macromol. B, 2001, Vol: 339, pages 204-238.
U{DOI:
10.1016/S0076-6879(01)39315-1<http://dx.doi.org/10.1016/S0076-6879%2801%2939315-1>}
Modified:
trunk/specific_analyses/relax_disp/parameters.py
Modified: trunk/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameters.py?rev=25024&r1=25023&r2=25024&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/parameters.py (original)
+++ trunk/specific_analyses/relax_disp/parameters.py Fri Aug 15 15:11:00
2014
@@ -34,7 +34,7 @@
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin
from specific_analyses.relax_disp.data import count_spins, generate_r20_key,
has_exponential_exp_type, loop_cluster, loop_exp_frq
-from specific_analyses.relax_disp.variables import MODEL_LIST_MMQ,
MODEL_M61B, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, PARAMS_R20
+from specific_analyses.relax_disp.variables import
MODEL_LIST_ANALYTIC_R1RHO, MODEL_LIST_CPMG_ONLY, MODEL_LIST_MMQ,
MODEL_LIST_NUMERIC_R1RHO, MODEL_M61B, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR,
PARAMS_R20
def assemble_param_vector(spins=None, key=None, sim_index=None):
@@ -435,6 +435,12 @@
def linear_constraints(spins=None, scaling_matrix=None):
"""Set up the relaxation dispersion curve fitting linear constraint
matrices A and b.
+ The suggested restraints for 'kex' follows from article, on page 224:
+ Nuclear Magnetic Resonance Methods for Quantifying
Microsecond-to-Millisecond Motions in Biological Macromolecules.
+ Palmer-III, Arthur G., Kroenke, Christopher D., Loria, J. Patrick
+ Nucl. Magn. Reson. Biol. Macromol. B, 2001, Vol: 339, pages 204-238.
+ U{DOI:
10.1016/S0076-6879(01)39315-1<http://dx.doi.org/10.1016/S0076-6879%2801%2939315-1>}.
+
Standard notation
=================
@@ -453,12 +459,12 @@
phi_ex_C >= 0
padw2 >= 0
dw >= 0
- 0 <= kex <= 2e6
- 0 <= k_AB <= 2e6
- 0 <= kB <= 2e6
- 0 <= kC <= 2e6
+ 0 <= kex <= 1e4, for CPMG
+ 0 <= kex <= 1e5, for R1rho
+ 0 <= k_AB <= 1e4
+ 0 <= kB <= 1e4
+ 0 <= kC <= 1e4
tex >= 0
- k_AB >= 0
Matrix notation
@@ -502,19 +508,22 @@
| | | | | |
| 1 0 0 | | kex | | 0 |
| | | | | |
- |-1 0 0 | | kex | | -2e6 |
+ |-1 0 0 | | kex | |-1e4/-1e5|
+ | | | | | |
+ | 1 0 0 | | k_AB | | 0 |
+ | | | | | |
+ |-1 0 0 | | k_AB | | -1e4 |
| | | | | |
| 1 0 0 | | kB | | 0 |
| | | | | |
- |-1 0 0 | | kB | | -2e6 |
+ |-1 0 0 | | kB | | -1e4 |
| | | | | |
| 1 0 0 | | kC | | 0 |
| | | | | |
- |-1 0 0 | | kC | | -2e6 |
+ |-1 0 0 | | kC | | -1e4 |
| | | | | |
| 1 0 0 | | tex | | 0 |
| | | | | |
- | 1 0 0 | | k_AB | | 0 |
@keyword spins: The list of spin data containers for the
block.
@@ -628,14 +637,21 @@
j += 1
break
- # Exchange rates and times (0 <= k <= 2e6).
+ # Exchange rates and times (0 <= k <= 1e4) for CPMG and (0 <= k <=
1e5) for R1rho.
elif param_name in ['kex', 'kex_AB', 'kex_AC', 'kex_BC', 'k_AB',
'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])
+ # For CPMG experiments, (0 <= k <= 1e4).
+ if spins[0].model in MODEL_LIST_CPMG_ONLY + MODEL_LIST_MMQ:
+ b.append(-1e4 / scaling_matrix[param_index, param_index])
+ # For R1rho experiments, (0 <= k <= 1e5).
+ elif spins[0].model in MODEL_LIST_ANALYTIC_R1RHO +
MODEL_LIST_NUMERIC_R1RHO:
+ b.append(-1e5 / scaling_matrix[param_index, param_index])
+ else:
+ b.append(-2e6 / scaling_matrix[param_index, param_index])
j += 2
# Exchange times (tex >= 0).
r25024 - /trunk/specific_analyses/relax_disp/parameters.py