Hi,
Actually, it is quite dangerous to the average parameter value, as
they can start arbitrary values if the user uses the value.set() user
function. This worked in the relaxation curve fitting for the peak
heights, but that was a lucky exception. It's best to have fixed
values here as you know roughly what order of magnitude the end values
should be (from Flemming's data). It's best to look how the
model-free assemble_scaling_matrix() method does this.
Regards,
Edward
On Tue, Jan 13, 2009 at 2:51 PM, <sebastien.morin.1@xxxxxxxxx> wrote:
Author: semor
Date: Tue Jan 13 14:51:31 2009
New Revision: 8430
URL: http://svn.gna.org/viewcvs/relax?rev=8430&view=rev
Log:
Completed the scaling matrix code.
This follows a thread at:
https://mail.gna.org/public/relax-devel/2009-01/msg00073.html
(Message-id: <496C09F1.1000307@xxxxxxxxx>)
Modified:
branches/relax_disp/specific_fns/relax_disp.py
Modified: branches/relax_disp/specific_fns/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8430&r1=8429&r2=8430&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/relax_disp.py (original)
+++ branches/relax_disp/specific_fns/relax_disp.py Tue Jan 13 14:51:31 2009
@@ -149,11 +149,55 @@
pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
# Scaling.
- scaling_matrix[i, i] = 1.0 / average(spin.r2effs[pos])
-
- # No scaling for other parameters.
- else:
- pass
+ scaling_matrix[i, i] = 1.0 / average(spin.r2eff[pos])
+
+ # Transversal relaxation rate scaling.
+ elif spin.params[i] == 'R2':
+ # Find the position of the first CPMG pulse train
frequency point.
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
+
+ # Scaling.
+ scaling_matrix[i, i] = 1.0 / average(spin.r2[pos])
+
+ # Chemical exchange contribution to 'R2' scaling.
+ elif spin.params[i] == 'Rex':
+ # Find the position of the first CPMG pulse train
frequency point.
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
+
+ # Scaling.
+ scaling_matrix[i, i] = 1.0 / average(spin.rex[pos])
+
+ # Exchange rate scaling.
+ elif spin.params[i] == 'kex':
+ # Find the position of the first CPMG pulse train
frequency point.
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
+
+ # Scaling.
+ scaling_matrix[i, i] = 1.0 / average(spin.kex[pos])
+
+ # Transversal relaxation rate for state A scaling
+ elif spin.params[i] == 'R2A':
+ # Find the position of the first CPMG pulse train
frequency point.
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
+
+ # Scaling.
+ scaling_matrix[i, i] = 1.0 / average(spin.r2a[pos])
+
+ # Exchange rate from state A to state B scaling.
+ elif spin.params[i] == 'kA':
+ # Find the position of the first CPMG pulse train
frequency point.
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
+
+ # Scaling.
+ scaling_matrix[i, i] = 1.0 / average(spin.ka[pos])
+
+ # Chemical shift difference between states A and B scaling.
+ elif spin.params[i] == 'dw':
+ # Find the position of the first CPMG pulse train
frequency point.
+ pos = cdp.cpmg_frqs.index(min(cdp.cpmg_frqs))
+
+ # Scaling.
+ scaling_matrix[i, i] = 1.0 / average(spin.dw[pos])
# Increment i.
i = i + 1
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Re: r8430 - /branches/relax_disp/specific_fns/relax_disp.py