Author: tlinnet Date: Wed Aug 20 22:01:05 2014 New Revision: 25128 URL: http://svn.gna.org/viewcvs/relax?rev=25128&view=rev Log: Reverted r25024, related to Linear Constraints change. The command used was: svn merge -r25024:r25023 . ........ r25024 | tlinnet | 2014-08-15 15:11:00 +0200 (Fri, 15 Aug 2014) | 11 lines 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=25128&r1=25127&r2=25128&view=diff ============================================================================== --- trunk/specific_analyses/relax_disp/parameters.py (original) +++ trunk/specific_analyses/relax_disp/parameters.py Wed Aug 20 22:01:05 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, is_r1_optimised, loop_cluster, loop_exp_frq -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 +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 def assemble_param_vector(spins=None, key=None, sim_index=None): @@ -425,12 +425,6 @@ 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 ================= @@ -449,12 +443,12 @@ phi_ex_C >= 0 padw2 >= 0 dw >= 0 - 0 <= kex <= 1e4, for CPMG - 0 <= kex <= 1e5, for R1rho - 0 <= k_AB <= 1e4 - 0 <= kB <= 1e4 - 0 <= kC <= 1e4 + 0 <= kex <= 2e6 + 0 <= k_AB <= 2e6 + 0 <= kB <= 2e6 + 0 <= kC <= 2e6 tex >= 0 + k_AB >= 0 Matrix notation @@ -498,22 +492,19 @@ | | | | | | | 1 0 0 | | kex | | 0 | | | | | | | - |-1 0 0 | | kex | |-1e4/-1e5| + |-1 0 0 | | kex | | -2e6 | + | | | | | | + | 1 0 0 | | kB | | 0 | + | | | | | | + |-1 0 0 | | kB | | -2e6 | + | | | | | | + | 1 0 0 | | kC | | 0 | + | | | | | | + |-1 0 0 | | kC | | -2e6 | + | | | | | | + | 1 0 0 | | tex | | 0 | | | | | | | | 1 0 0 | | k_AB | | 0 | - | | | | | | - |-1 0 0 | | k_AB | | -1e4 | - | | | | | | - | 1 0 0 | | kB | | 0 | - | | | | | | - |-1 0 0 | | kB | | -1e4 | - | | | | | | - | 1 0 0 | | kC | | 0 | - | | | | | | - |-1 0 0 | | kC | | -1e4 | - | | | | | | - | 1 0 0 | | tex | | 0 | - | | | | | | @keyword spins: The list of spin data containers for the block. @@ -627,21 +618,14 @@ j += 1 break - # Exchange rates and times (0 <= k <= 1e4) for CPMG and (0 <= k <= 1e5) for R1rho. + # Exchange rates and times (0 <= k <= 2e6). 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) - # 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]) + b.append(-2e6 / scaling_matrix[param_index, param_index]) j += 2 # Exchange times (tex >= 0).