Re: r24942 - /branches/R1_fitting/specific_analyses/relax_disp/variables.py -- August 18, 2014

Hi Troels,

Pity I couldn't see this early to discuss it.  But the
MODEL_NOREX_R1RHO model should be merged into MODEL_NOREX.  We can
make the decision for the user if on or off-resonance is handled.
This again is for the future support of off-resonance effects in the
CPMG experiments.  Part of the relax design is to minimise what is
presented to the user.  If they select the 'No Rex' model, then this
model should work for on-resonance and off-resonance R1rho data, as
well as CPMG data, without them having to think about it.  We are
fully capable of handling this in the backend for the user.

'No Rex' is simple for a user to understand as it means no chemical
exchange.  Having multiple 'No Rex' models will be confusing.
Allowing R1 to be optimised via another 'No Rex' model could be
useful.  Though again we can handle this in the backend - if no R1
data is present, we present a warning "No R1 data has been loaded,
optimising this as a parameter of the model" and then just optimise it
for them.  The backend would just have a few different target
functions for the same model.  The simpler we make the interface for
the user, without taking away any functionality, the more powerful the
software will become.

Cheers,

Edward


On 4 August 2014 19:22,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Mon Aug  4 19:22:04 2014
New Revision: 24942

URL: http://svn.gna.org/viewcvs/relax?rev=24942&view=rev
Log:
Added 2 new models, MODEL_NOREX_R1RHO and MODEL_NOREX_R1RHO_FIT_R1.

The "NOREX" model is not covering R1rho models.
The target function for "NOREX" is calculated as:
back_calc = R20

R20 is for R1hro models equivalent to R1rho prime (R1rho'), which for 
example in the model of DPL94 would mean:
R1rho = R1rho'

But for the "NOREX" case, the return should be
R1rho = R1 * cos^2(theta) + (R1rho' + 0) * sin^2(theta)

This affects all off-resonance model calculations.

These two target functions will be implemented.

bug #22440(https://gna.org/bugs/?22440): The "NOREX" model is not covering 
R1rho models.
sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation 
rate for the off-resonance R1rho relaxation dispersion models.

Modified:
    branches/R1_fitting/specific_analyses/relax_disp/variables.py

Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/variables.py?rev=24942&r1=24941&r2=24942&view=diff
==============================================================================
--- branches/R1_fitting/specific_analyses/relax_disp/variables.py       
(original)
+++ branches/R1_fitting/specific_analyses/relax_disp/variables.py       Mon 
Aug  4 19:22:04 2014
@@ -64,6 +64,14 @@
 MODEL_DESC_NOREX = "The model for no chemical exchange relaxation."
 MODEL_PARAMS_NOREX = ['r2']

+MODEL_NOREX_R1RHO = "No_Rex_R1rho_off_res"
+MODEL_DESC_NOREX_R1RHO = "The model for no chemical exchange relaxation, 
for R1rho off resonance models."
+MODEL_PARAMS_NOREX_R1RHO = ['r2']
+
+MODEL_NOREX_R1RHO_FIT_R1 = "%s_fit_r1"%MODEL_NOREX_R1RHO
+MODEL_DESC_NOREX_R1RHO_FIT_R1 = "The model for no chemical exchange 
relaxation, for R1rho off resonance models, where R1 is fitted."
+MODEL_PARAMS_NOREX_R1RHO_FIT_R1 = ['r1_fit', 'r2']
+
 MODEL_LM63 = 'LM63'
 MODEL_DESC_LM63 = "The Luz and Meiboom (1963) 2-site fast exchange model 
for SQ-CPMG experiments."
 MODEL_PARAMS_LM63 = ['r2', 'phi_ex', 'kex']
@@ -196,16 +204,16 @@
 MODEL_LIST_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, 
MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, 
MODEL_B14, MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_3D, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED]
 """The list of the R2eff model together with all dispersion models 
specifically for CPMG-type experiments."""

-MODEL_LIST_R1RHO = [MODEL_NOREX, MODEL_M61, MODEL_M61B, MODEL_DPL94, 
MODEL_DPL94_FIT_R1, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
+MODEL_LIST_R1RHO = [MODEL_NOREX, MODEL_NOREX_R1RHO, 
MODEL_NOREX_R1RHO_FIT_R1, MODEL_M61, MODEL_M61B, MODEL_DPL94, 
MODEL_DPL94_FIT_R1, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
 """The list of all dispersion models specifically for R1rho-type 
experiments (excluding the R2eff model)."""

-MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_M61B, 
MODEL_DPL94, MODEL_DPL94_FIT_R1, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
+MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_NOREX_R1RHO, 
MODEL_NOREX_R1RHO_FIT_R1, MODEL_M61, MODEL_M61B, MODEL_DPL94, 
MODEL_DPL94_FIT_R1, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
 """The list of the R2eff model together with all dispersion models 
specifically for R1rho-type experiments."""

-MODEL_LIST_R1RHO_W_R1 = [MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 
MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
+MODEL_LIST_R1RHO_W_R1 = [MODEL_NOREX_R1RHO, MODEL_DPL94, MODEL_TP02, 
MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, 
MODEL_NS_R1RHO_3SITE_LINEAR]
 """The list of all dispersion models specifically for R1rho-type 
experiments which use R1 in their equations."""

-MODEL_LIST_R1RHO_FIT_R1 = [MODEL_DPL94_FIT_R1]
+MODEL_LIST_R1RHO_FIT_R1 = [MODEL_NOREX_R1RHO_FIT_R1, MODEL_DPL94_FIT_R1]
 """The list of all dispersion models specifically for R1rho-type 
experiments which fit R1 in their equations."""

 MODEL_LIST_MQ_CPMG = [MODEL_NOREX, MODEL_MMQ_CR72, MODEL_NS_MMQ_2SITE, 
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]
@@ -245,6 +253,8 @@
 MODEL_DESC = {
     MODEL_R2EFF: MODEL_DESC_R2EFF,
     MODEL_NOREX: MODEL_DESC_NOREX,
+    MODEL_NOREX_R1RHO: MODEL_DESC_NOREX_R1RHO,
+    MODEL_NOREX_R1RHO_FIT_R1: MODEL_DESC_NOREX_R1RHO_FIT_R1,
     MODEL_LM63: MODEL_DESC_LM63,
     MODEL_LM63_3SITE: MODEL_DESC_LM63_3SITE,
     MODEL_CR72: MODEL_DESC_CR72,
@@ -278,6 +288,8 @@
 MODEL_PARAMS = {
     MODEL_R2EFF: MODEL_PARAMS_R2EFF,
     MODEL_NOREX: MODEL_PARAMS_NOREX,
+    MODEL_NOREX_R1RHO: MODEL_PARAMS_NOREX_R1RHO,
+    MODEL_NOREX_R1RHO_FIT_R1: MODEL_PARAMS_NOREX_R1RHO_FIT_R1,
     MODEL_LM63: MODEL_PARAMS_LM63,
     MODEL_LM63_3SITE: MODEL_PARAMS_LM63_3SITE,
     MODEL_CR72: MODEL_PARAMS_CR72,


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Re: r24942 - /branches/R1_fitting/specific_analyses/relax_disp/variables.py

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