Hi Troels, I am unable to download that reference and the book with the reference in Goettingen is 500 km away from where I am now. Would you be able to send me a copy in a private mail? Cheers.
I'm not convinced that this change should be made. The constraint of 1e6 was simply a large upper bound whereby no exchange should be visible. The constraint is used to prevent kex from heading out to infinity. So changing it to 1e4 or 1e5 will have no effect on this purpose of the constraint. What worries me here is that although exchange is very close to zero at these new limits, they are not exactly zero. This is especially the case for data with very, very small errors (test data with zero errors will show this). So the edge cases you have mapped out with OpenDX (https://gna.org/bugs/?22024 for example) will be highly effected by such a change. But this would be an edge case on the other side of the space. The new limits could chop a very weak minimum out of the optimisation space - i.e. you've put up a wall in front of these weak minima. This is a very weak edge case, but it nevertheless exists. As the purpose of the constraint is simply to stop kex from going to infinity, loosing these special edge case minima is not worth it. I would suggest reverting this change. Cheers, Edward On 15 August 2014 15:11, <[email protected]> wrote: > 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). > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
