Re: r25024 - /trunk/specific_analyses/relax_disp/parameters.py -- August 19, 2014

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,  <tlinnet@xxxxxxxxxxxxx> 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).


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Re: r25024 - /trunk/specific_analyses/relax_disp/parameters.py

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