r21879 - /trunk/docs/latex/dispersion.tex
Author: bugman Date: Mon Dec 9 09:09:48 2013 New Revision: 21879 URL: http://svn.gna.org/viewcvs/relax?rev=21879view=rev Log: Large rearrangements in the dispersion chapter of the user manual. The MMQ CPMG-type experiments now follow from the SQ CPMG-type experiments, hence the R1rho models are now listed last. Modified: trunk/docs/latex/dispersion.tex [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/docs/latex/dispersion.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21879r1=21878r2=21879view=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21880 - in /trunk/docs/latex: bibliography.bib dispersion.tex
Author: bugman
Date: Mon Dec 9 09:21:52 2013
New Revision: 21880
URL: http://svn.gna.org/viewcvs/relax?rev=21880view=rev
Log:
Added a To do entry for the 3-site and N-site analytic R1rho models listed in
Palmer and Massi 2006.
This is for the 'To do' section of the dispersion chapter of the user manual.
Modified:
trunk/docs/latex/bibliography.bib
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/bibliography.bib
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/bibliography.bib?rev=21880r1=21879r2=21880view=diff
==
--- trunk/docs/latex/bibliography.bib (original)
+++ trunk/docs/latex/bibliography.bib Mon Dec 9 09:21:52 2013
@@ -30,6 +30,9 @@
% The Computer Journal.
@STRING{cj = Comp. J.}
+
+% Chemistry Review.
+@STRING{cr = Chem. Rev.}
% European Journal of Biochemistry.
@STRING{ejb = Eur. J. Biochem.}
@@ -5959,6 +5962,53 @@
doi= {10.1021/ja00012a001}
}
+@Article{PalmerMassi06,
+ Author = {Palmer, 3rd, A. G. and Massi, F.},
+ Title = {Characterization of the dynamics of biomacromolecules
+ using rotating-frame spin relaxation {NMR}
+ spectroscopy.},
+ Journal= cr,
+ Volume = {106},
+ Number = {5},
+ Pages = {1700-1719},
+ authoraddress = {Department of Biochemistry and Molecular Biophysics,
+ Columbia University, 630 West 168th Street, New York,
+ New York 10032, USA. a...@columbia.edu},
+ keywords = {Kinetics ; Ligands ; Macromolecular
+ Substances/chemistry ; Magnetic Resonance
+ Spectroscopy/methods ; *Models, Chemical ; Molecular
+ Structure ; Multiprotein Complexes/chemistry ; Protein
+ Conformation ; Water/chemistry},
+ language = {eng},
+ medline-aid= {10.1021/cr0404287 [doi]},
+ medline-crdt = {2006/05/11 09:00},
+ medline-da = {20060510},
+ medline-dcom = {20071113},
+ medline-edat = {2006/05/11 09:00},
+ medline-fau= {Palmer, Arthur G 3rd ; Massi, Francesca},
+ medline-gr = {GM59273/GM/NIGMS NIH HHS/United States},
+ medline-is = {0009-2665 (Print) ; 0009-2665 (Linking)},
+ medline-jid= {2985134R},
+ medline-jt = {Chemical reviews},
+ medline-lr = {20071203},
+ medline-mhda = {2007/11/14 09:00},
+ medline-own= {NLM},
+ medline-pl = {United States},
+ medline-pmid = {16683750},
+ medline-pst= {ppublish},
+ medline-pt = {Journal Article ; Research Support, N.I.H., Extramural
+ ; Review},
+ medline-rf = {78},
+ medline-rn = {0 (Ligands) ; 0 (Macromolecular Substances) ; 0
+ (Multiprotein Complexes) ; 7732-18-5 (Water)},
+ medline-sb = {IM},
+ medline-so = {Chem Rev. 2006 May;106(5):1700-19.},
+ medline-stat = {MEDLINE},
+ url=
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinksdbfrom=pubmedretmode=refid=16683750},
+ doi= {10.1021/cr0404287},
+ year = 2006
+}
+
@Article{Pawley01,
Author = {Pawley, N. H. and Wang, C. and Koide, S. and
Nicholson, L. K.},
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21880r1=21879r2=21880view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 09:21:52 2013
@@ -1598,6 +1598,7 @@
\item[`TP04':]\index{relaxation dispersion!TP04 model} The $\Ronerho$-type
data \citet{TrottPalmer04} N-site analytic equation for all time scales with
parameters $\{\Ronerhoprime, \dots, \pone, \dots, \pN, \aveomega, \konetwo,
\dots\, \koneN\}$.
\item[`NS $\Ronerho$ 3-site linear':]\index{relaxation dispersion!NS R1rho
3-site linear model} The model of the numeric solution for linear 3-site
exchange for $\Ronerho$-type data.
\item[`NS $\Ronerho$ 3-site':]\index{relaxation dispersion!NS R1rho 3-site
model} Similar to the `NS $\Ronerho$ 3-site linear' model but with one of the
$\kex$ parameters not set to zero.
+\item[`* $\Ronerho$':] All of the 3-site and N-site models as summarised in
Table~1 of \citet{PalmerMassi}.
\end{description}
Information for how these can be added is given in the next section.
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r21882 - /trunk/lib/dispersion/ns_r1rho_2site.py
Author: bugman
Date: Mon Dec 9 10:05:19 2013
New Revision: 21882
URL: http://svn.gna.org/viewcvs/relax?rev=21882view=rev
Log:
Updated the lib.dispersion.ns_r1rho_2site module docstring to explain the
origin of the equations.
This includes the Korzhnev 2005 reference where the modifications come from.
Modified:
trunk/lib/dispersion/ns_r1rho_2site.py
Modified: trunk/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_2site.py?rev=21882r1=21881r2=21882view=diff
==
--- trunk/lib/dispersion/ns_r1rho_2site.py (original)
+++ trunk/lib/dispersion/ns_r1rho_2site.py Mon Dec 9 10:05:19 2013
@@ -25,6 +25,12 @@
This function performs a numerical fit of 2-site Bloch-McConnell equations
for R1rho-type experiments.
This is the model of the numerical solution for the 2-site Bloch-McConnell
equations. It originates from the funNumrho.m file from the Skrynikov
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
+
+The solution has been modified to use the from presented in:
+
+- Korzhnev, D. M., Orekhov, V. Y., and Kay, L. E. (2005). Off-resonance
R(1rho) NMR
+studies of exchange dynamics in proteins with low spin-lock fields: an
application to a
+Fyn SH3 domain. J. Am. Chem. Soc., 127, 713-721. (U{DOI:
10.1021/ja0446855http://dx.doi.org/10.1021/ja0446855}).
# Dependency check module.
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r21883 - in /trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear: ./ blank/ cpmg_fit_results/ relax_results/
Author: bugman Date: Mon Dec 9 11:04:33 2013 New Revision: 21883 URL: http://svn.gna.org/viewcvs/relax?rev=21883view=rev Log: Created some synthetic data for the 'NS R1rho 3-site linear' dispersion model using cpmg_fit. Added: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/ - copied from r21876, trunk/test_suite/shared_data/dispersion/ns_mmq_3site_linear/ trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_5500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_6000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_75.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_5500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_6000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_75.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/R1_600MHz.out - copied, changed from r21876, trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/R1_600MHz.out trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/R1_800MHz.out - copied, changed from r21876, trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/R1_800MHz.out trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/all.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_4500.res
r21884 - /trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/
Author: bugman Date: Mon Dec 9 11:11:29 2013 New Revision: 21884 URL: http://svn.gna.org/viewcvs/relax?rev=21884view=rev Log: Added cpmg_fit results for the Fyn SH3 R1rho test suite data using the 3-site numeric solution. Added: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site.in - copied, changed from r21876, trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.in trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.in - copied, changed from r21876, trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.in trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.log Copied: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site.in (from r21876, trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.in) URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site.in?p2=trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site.inp1=trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.inr1=21876r2=21884rev=21884view=diff == --- trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.in (original) +++ trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site.in Mon Dec 9 11:11:29 2013 @@ -11,16 +11,20 @@ # Set up the model. set m 3 0 -# Set the parameters. -set p @ 0 0.999 u -set p @ 1 0.06250456703 u -set k @ 0 346.593135661913038 u +# Set the parameters (at the already found minimum). +set p @ 0 0.576531903402283 u +set p @ 1 0.036871721967958 u +set p @ 2 0.386596374629759 u +set k @ 0 349.172677335404501 u +set k @ 1 4.494230664781980 u +set k @ 2 4.494230664781980 u set c @ @ 0 0 0 f -set c @ @ 1 0 4.314915278589107 u -set r @ R N15 25 600 @ 7.513382903549340 u g -set l @ N15 25 600 @ 1.603317143873361 u g -set r @ R N15 25 800 @ 12.247154287911538 u g -set l @ N15 25 800 @ 2.836630130629836 u g +set c @ @ 1 0 4.307941328122205 u +set c @ @ 2 0 -1.614739454824554 u +set r @ R N15 25 600 @ 5.529350411646063 u g +set l @ N15 25 600 @ 0.87239821652 u g +set r @ R N15 25 800 @ 10.399050915057499 u g +set l @ N15 25 800 @ 1.267443569515087 u g # Minimisation. min Copied: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.in (from r21876, trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.in) URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.in?p2=trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.inp1=trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.inr1=21876r2=21884rev=21884view=diff == --- trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_2site.in (original) +++ trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.in Mon Dec 9 11:11:29 2013 @@ -11,16 +11,19 @@ # Set up the model. set m 3 0 -# Set the parameters. -set p @ 0 0.999 u -set p @ 1 0.06250456703 u -set k @ 0 346.593135661913038 u +# Set the parameters (at the already found minimum). +set p @ 0 0.576531903402283 u +set p @ 1 0.036871721967958 u +set p @ 2 0.386596374629759 u +set k @ 0 349.172677335404501 u +set k @ 1 4.494230664781980 u set c @ @ 0 0 0 f -set c @ @ 1 0 4.314915278589107 u -set r @ R N15 25 600 @ 7.513382903549340 u g -set l @ N15 25 600 @ 1.603317143873361 u g -set r @ R N15 25 800 @ 12.247154287911538 u g -set l @ N15 25 800 @ 2.836630130629836 u g +set c @ @ 1 0 4.307941328122205 u +set c @ @ 2 0 1.614739454824554 u +set r @ R N15 25 600 @ 5.529350411646063 u g +set l @ N15 25 600 @ 1.625350776218974 f g +set r @ R N15 25 800 @ 10.399050915057499 u g +set l @ N15 25 800 @ 2.879266198836596 f g # Minimisation. min Added: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.log?rev=21884view=auto == --- trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.log (added) +++ trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/cpmg_fit_results/ns_r1rho_3site_linear.log Mon Dec 9 11:11:29 2013 @@ -1,0 +1,32 @@ + Max. number of
r21885 - in /trunk/test_suite/system_tests: relax_disp.py scripts/relax_disp/ns_r1rho_3site_linear.py
Author: bugman
Date: Mon Dec 9 11:13:17 2013
New Revision: 21885
URL: http://svn.gna.org/viewcvs/relax?rev=21885view=rev
Log:
Created the Relax_disp.test_ns_r1rho_3site_linear system test.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite
Added:
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
- copied, changed from r21883,
trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21885r1=21884r2=21885view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 11:13:17 2013
@@ -2440,6 +2440,16 @@
self.assertAlmostEqual(cdp.mol[0].res[0].spin[1].chi2, 0.0, 3)
+def test_ns_r1rho_3site_linear(self):
+Compare the 'NS R1rho 3-site linear' dispersion model to synthetic
data from cpmg_fit.
+
+# Execute the script.
+self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_r1rho_3site_linear.py')
+
+# Check the chi-squared value.
+self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 0.0, 3)
+
+
def test_r2eff_read(self):
Test the operation of the relax_disp.r2eff_read user function.
Copied:
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py (from
r21883,
trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py?p2=trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.pyp1=trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.pyr1=21883r2=21885rev=21885view=diff
==
---
trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
Mon Dec 9 11:13:17 2013
@@ -1,14 +1,18 @@
-Compare the synthetic cpmg_fit data to the relax solution.
+Compare the synthetic cpmg_fit data to the relax solution.
-To run this, type:
-
-$ rm -f solution.log; ../../../../../relax --tee solution.log solution.py
-
+# Python module imports.
+from os import sep
# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
from lib.nmr import frequency_to_ppm
from specific_analyses.relax_disp.disp_data import generate_r20_key
from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO
+from status import Status; status = Status()
+
+
+# The path to the data files.
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'ns_r1rho_3site_linear'
# Create a data pipe.
@@ -85,11 +89,11 @@
relax_disp.spin_lock_offset(spectrum_id=new_id,
offset=-frequency_to_ppm(frq=offset, B0=H_frq, isotope='15N'))
# Read the R2eff data.
-relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=':1',
offset_col=6, data_col=10, error_col=9)
+relax_disp.r2eff_read_spin(id=id, file=file, dir=DATA_PATH, spin_id=':1',
offset_col=6, data_col=10, error_col=9)
# Load the R1 data.
-relax_data.read(ri_id='600MHz', ri_type='R1', frq=600e6, file='R1_600MHz.out',
dir='..', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
-relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out',
dir='..', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='600MHz', ri_type='R1', frq=600e6, file='R1_600MHz.out',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
# Change the model.
relax_disp.select_model('NS R1rho 3-site')
@@ -117,12 +121,8 @@
# Calculate.
calc()
-# Minimisation.
-grid_search(inc=7)
-minimise('simplex', constraints=True)
-
# Plot the dispersion curves.
-relax_disp.plot_disp_curves(dir='.', num_points=100, extend=0, force=True)
+relax_disp.plot_disp_curves(dir=ds.tmpdir, num_points=100, extend=0,
force=True)
# Save the results.
-state.save('state', dir='.',
r21886 - /trunk/specific_analyses/relax_disp/variables.py
Author: bugman Date: Mon Dec 9 11:16:57 2013 New Revision: 21886 URL: http://svn.gna.org/viewcvs/relax?rev=21886view=rev Log: Added the 'NS R1rho 3-site' models to the dispersion variables. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list Modified: trunk/specific_analyses/relax_disp/variables.py Modified: trunk/specific_analyses/relax_disp/variables.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/variables.py?rev=21886r1=21885r2=21886view=diff == --- trunk/specific_analyses/relax_disp/variables.py (original) +++ trunk/specific_analyses/relax_disp/variables.py Mon Dec 9 11:16:57 2013 @@ -117,6 +117,13 @@ MODEL_NS_R1RHO_2SITE = 'NS R1rho 2-site' The numerical solution for the 2-site Bloch-McConnell equations for R1rho data, whereby the simplification R20A = R20B is assumed. +MODEL_NS_R1RHO_3SITE = 'NS R1rho 3-site' +The numerical solution for the 3-site Bloch-McConnell equations for R1rho data, whereby the simplification R20A = R20B = R20C is assumed. + +MODEL_NS_R1RHO_3SITE_LINEAR = 'NS R1rho 3-site' +The numerical solution for the 3-site Bloch-McConnell equations for R1rho data linearised with kAC = kCA = 0, whereby the simplification R20A = R20B = R20C is assumed. + + # The multi-quantum data model names. MODEL_MMQ_CR72 = 'MMQ CR72' The Carver and Richards (1972) 2-site model for all time scales extended for MMQ CPMG data. @@ -132,10 +139,10 @@ # The model lists. -MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, MODEL_M61, MODEL_M61B, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 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, MODEL_NS_R1RHO_2SITE, MODEL_MMQ_CR72, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR] +MODEL_LIST_DISP = [MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, MODEL_M61, MODEL_M61B, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 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, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_MMQ_CR72, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR] The list of all dispersion models (excluding the R2eff model). -MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, MODEL_M61, MODEL_M61B, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 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, MODEL_NS_R1RHO_2SITE, MODEL_MMQ_CR72, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR] +MODEL_LIST_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, MODEL_M61, MODEL_M61B, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, 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, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_MMQ_CR72, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR] The list of the R2eff model together with all dispersion models. MODEL_LIST_CPMG = [MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, 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] @@ -144,10 +151,10 @@ MODEL_LIST_CPMG_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_TSMFK01, 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_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE] +MODEL_LIST_R1RHO = [MODEL_NOREX, MODEL_M61, MODEL_M61B, 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 (excluding the R2eff model). -MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61, MODEL_M61B, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05,
r21887 - /trunk/user_functions/relax_disp.py
Author: bugman
Date: Mon Dec 9 11:23:07 2013
New Revision: 21887
URL: http://svn.gna.org/viewcvs/relax?rev=21887view=rev
Log:
Added the 'NS R1rho 3-site' models to the relax_disp.select_model user function
frontend.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end
Modified:
trunk/user_functions/relax_disp.py
Modified: trunk/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=21887r1=21886r2=21887view=diff
==
--- trunk/user_functions/relax_disp.py (original)
+++ trunk/user_functions/relax_disp.py Mon Dec 9 11:23:07 2013
@@ -42,7 +42,7 @@
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_MMQ_CR72, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE,
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE,
MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_MMQ_CR72, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE,
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_R2EFF, MODEL_TAP03,
MODEL_TP02, MODEL_TSMFK01
from specific_analyses.setup import relax_disp_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -817,6 +817,8 @@
%s: {%s, ..., pA, %s, %s} % (MODEL_TAP03, r1rho_prime, dw, kex),
%s: {%s, ..., pA, %s, %s} % (MODEL_MP05, r1rho_prime, dw, kex),
%s: {%s, ..., pA, %s, %s} % (MODEL_NS_R1RHO_2SITE, r1rho_prime, dw,
kex),
+%s: {%s, ..., pA, %s, %s, pB, %s, %s} %
(MODEL_NS_R1RHO_3SITE_LINEAR, r2, dw_AB, kAB, dw_BC, kBC),
+%s: {%s, ..., pA, %s, %s, pB, %s, %s, %s} % (MODEL_NS_R1RHO_3SITE,
r2, dw_AB, kAB, dw_BC, kBC, kAC),
%s: {%s, ..., pA, %s, %s, %s} % (MODEL_MMQ_CR72, r2, dw, dwH, kex),
%s: {%s, ..., pA, %s, %s, %s} % (MODEL_NS_MMQ_2SITE, r2, dw, dwH,
kex),
%s: {%s, ..., pA, %s, %s, %s, pB, %s, %s, %s} %
(MODEL_NS_MMQ_3SITE_LINEAR, r2, dw_AB, dwH_AB, kAB, dw_BC, dwH_BC, kBC),
@@ -843,6 +845,8 @@
MODEL_TAP03,
MODEL_MP05,
MODEL_NS_R1RHO_2SITE,
+MODEL_NS_R1RHO_3SITE_LINEAR,
+MODEL_NS_R1RHO_3SITE,
MODEL_MMQ_CR72,
MODEL_NS_MMQ_2SITE,
MODEL_NS_MMQ_3SITE_LINEAR,
@@ -880,7 +884,9 @@
uf.desc[-1].add_item_list_element('%s' % MODEL_TAP03, The Trott, Abergel
and Palmer (2003) off-resonance 2-site equation for all time scales with
parameters {R1rho', ..., pA, dw, kex}.)
uf.desc[-1].add_item_list_element('%s' % MODEL_MP05, The Miloushev and
Palmer (2005) 2-site off-resonance equation for all time scales with parameters
{R1rho', ..., pA, dw, kex}.)
uf.desc[-1].add_paragraph(The currently supported numeric models are:)
-uf.desc[-1].add_item_list_element('%s' % MODEL_NS_R1RHO_2SITE, The
numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors. Its parameters are {R1rho', ..., pA, dw, kex}.)
+uf.desc[-1].add_item_list_element('%s' % MODEL_NS_R1RHO_2SITE, The
numerical solution for the 2-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B = R20C is assumed
and linearised with kAC = kCA = 0. Its parameters are {R1rho', ..., pA,
dw(AB), kex(AB), pB, dw(BC), kex(BC)}.)
+uf.desc[-1].add_item_list_element('%s' % MODEL_NS_R1RHO_3SITE_LINEAR, The
numerical solution for the 3-site Bloch-McConnell equations using 3D
magnetisation vectors whereby the simplification R20A = R20B = R20C is assumed.
Its parameters are {R1rho', ..., pA, dw, kex}.)
+uf.desc[-1].add_item_list_element('%s' % MODEL_NS_R1RHO_3SITE, The
numerical solution for the 3-site
r21889 - /trunk/user_functions/relax_disp.py
Author: bugman
Date: Mon Dec 9 11:26:33 2013
New Revision: 21889
URL: http://svn.gna.org/viewcvs/relax?rev=21889view=rev
Log:
Changed the 'CPMG-type' to 'SQ CPMG-type' in the relax_disp.select_model user
function frontend.
Modified:
trunk/user_functions/relax_disp.py
Modified: trunk/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=21889r1=21888r2=21889view=diff
==
--- trunk/user_functions/relax_disp.py (original)
+++ trunk/user_functions/relax_disp.py Mon Dec 9 11:26:33 2013
@@ -860,7 +860,7 @@
uf.desc[-1].add_item_list_element('%s' % MODEL_R2EFF, This is the model
used to determine the R2eff/R1rho values and errors required as the base data
for all other models,)
uf.desc[-1].add_item_list_element('%s' % MODEL_NOREX, This is the model for
no chemical exchange being present.)
# CPMG-type data.
-uf.desc.append(Desc_container('The CPMG-type experiments'))
+uf.desc.append(Desc_container('The SQ CPMG-type experiments'))
uf.desc[-1].add_paragraph(The currently supported analytic models are:)
uf.desc[-1].add_item_list_element('%s' % MODEL_LM63, The original Luz and
Meiboom (1963) 2-site fast exchange equation with parameters {R20, ..., phi_ex,
kex},)
uf.desc[-1].add_item_list_element('%s' % MODEL_LM63_3SITE, The original Luz
and Meiboom (1963) 3-site fast exchange equation with parameters {R20, ...,
phi_ex, kex, phi_ex2, kex2},)
___
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r21890 - /trunk/specific_analyses/relax_disp/api.py
Author: bugman Date: Mon Dec 9 11:30:49 2013 New Revision: 21890 URL: http://svn.gna.org/viewcvs/relax?rev=21890view=rev Log: Added support for the 'NS R1rho 3-site' models to the relax_disp.select_model user function back end. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end. Modified: trunk/specific_analyses/relax_disp/api.py Modified: trunk/specific_analyses/relax_disp/api.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=21890r1=21889r2=21890view=diff == --- trunk/specific_analyses/relax_disp/api.py (original) +++ trunk/specific_analyses/relax_disp/api.py Mon Dec 9 11:30:49 2013 @@ -48,7 +48,7 @@ from specific_analyses.relax_disp.disp_data import average_intensity, find_intensity_keys, get_curve_type, has_exponential_exp_type, has_proton_mmq_cpmg, loop_cluster, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_frq, loop_time, pack_back_calc_r2eff, return_cpmg_frqs, return_index_from_disp_point, return_index_from_exp_type, return_index_from_frq, return_offset_data, return_param_key_from_data, return_r1_data, return_r2eff_arrays, return_spin_lock_nu1, spin_ids_to_containers from specific_analyses.relax_disp.optimisation import Disp_memo, Disp_minimise_command, back_calc_r2eff, grid_search_setup from specific_analyses.relax_disp.parameters import assemble_param_vector, assemble_scaling_matrix, disassemble_param_vector, get_param_names, get_value, linear_constraints, loop_parameters, param_index_to_param_info, param_num -from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_MMQ, MODEL_M61, MODEL_M61B, MODEL_MMQ_CR72, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 +from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_MMQ, MODEL_M61, MODEL_M61B, MODEL_MMQ_CR72, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 from target_functions.relax_disp import Dispersion from user_functions.data import Uf_tables; uf_tables = Uf_tables() from user_functions.objects import Desc_container @@ -604,6 +604,16 @@ print(The reduced numerical solution for the 2-site Bloch-McConnell equations for R1rho data using 3D magnetisation vectors, whereby the simplification R20A = R20B is assumed.) params = ['r2', 'pA', 'dw', 'kex'] +# NS R1rho CPMG 3-site model. +elif model == MODEL_NS_R1RHO_3SITE: +print(The numerical solution for the 3-site Bloch-McConnell equations for R1rho data using 3D magnetisation vectors whereby the simplification R20A = R20B = R20C is assumed.) +params = ['r2', 'pA', 'dw_AB', 'kex_AB', 'pB', 'dw_BC', 'kex_BC', 'kex_AC'] + +# NS R1rho CPMG 3-site linearised model. +elif model == MODEL_NS_R1RHO_3SITE_LINEAR: +print(The numerical solution for the 3-site Bloch-McConnell equations for R1rho data using 3D magnetisation vectors linearised with kAC = kCA = 0 whereby the simplification R20A = R20B = R20C is assumed.) +params = ['r2', 'pA', 'dw_AB', 'kex_AB', 'pB', 'dw_BC', 'kex_BC'] + # MMQ CR72 model. elif model == MODEL_MMQ_CR72: print(The Carver and Richards (1972) 2-site model for all time scales expanded for MMQ CPMG data by Korzhnev et al., 2004.) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21891 - in /trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear: ./ blank/ cpmg_fit_results/ relax_results/
Author: bugman Date: Mon Dec 9 11:50:03 2013 New Revision: 21891 URL: http://svn.gna.org/viewcvs/relax?rev=21891view=rev Log: Decreased the amount of synthetic data in the ns_r1rho_3site_linear test suite shared data directory. The number of offsets for this 'NS R1rho 3-site linear' model synthetic data has been decreased from 81 points to 21. This is because the large quantities of data slow the test suite down too much. Removed: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.log Modified: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_5500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_6000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/600_MHz_75.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_5500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_6000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/800_MHz_75.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/all.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/blank/600_MHz_5000.res
r21892 - /trunk/test_suite/gui_tests/relax_disp.py
Author: tlinnet Date: Mon Dec 9 11:50:20 2013 New Revision: 21892 URL: http://svn.gna.org/viewcvs/relax?rev=21892view=rev Log: Added GUI test for reading spins from a spectrum formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/gui_tests/relax_disp.py Modified: trunk/test_suite/gui_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/relax_disp.py?rev=21892r1=21891r2=21892view=diff == --- trunk/test_suite/gui_tests/relax_disp.py (original) +++ trunk/test_suite/gui_tests/relax_disp.py Mon Dec 9 11:50:20 2013 @@ -412,6 +412,43 @@ self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100) +def test_read_spins_from_spectrum(self): +Test the GUI load spins from a spectrum formatted file. + +# The path to the files. +path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'peak_lists' + sep + +# Simulate the dispersion analysis wizard. +self.app.gui.analysis.menu_new(None) +page = self.app.gui.analysis.new_wizard.wizard.get_page(0) +page.select_disp(None) +self.app.gui.analysis.new_wizard.wizard._go_next(None) +self.app.gui.analysis.new_wizard.wizard._go_next(None) + +# Get the data. +analysis_type, analysis_name, pipe_name, pipe_bundle, uf_exec = self.app.gui.analysis.new_wizard.get_data() + +# Set up the analysis. +self.app.gui.analysis.new_analysis(analysis_type=analysis_type, analysis_name=analysis_name, pipe_name=pipe_name, pipe_bundle=pipe_bundle, uf_exec=uf_exec) + +# Alias the analysis. +analysis = self.app.gui.analysis.get_page_from_name(Relaxation dispersion) + +# Change the results directory. +analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir)) + +# Launch the spin viewer window. +self.app.gui.show_tree() + +# Spin loading wizard: Initialisation. +self.app.gui.spin_viewer.load_spins_wizard() + +# Spin loading wizard: The spectrum.read_spins page. +page = self.app.gui.spin_viewer.wizard.get_page(0) +page.selection = 'new spectrum' +self.app.gui.spin_viewer.wizard._go_next() + + def test_tp02_data_to_tp02(self): Test the GUI analysis with the relaxation dispersion 'TP02' model fitting to the 'TP02' synthetic data. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21893 - /trunk/gui/spin_viewer/frame.py
Author: tlinnet Date: Mon Dec 9 11:50:33 2013 New Revision: 21893 URL: http://svn.gna.org/viewcvs/relax?rev=21893view=rev Log: Added GUI key 'new spectrum' to point to 'spectrum.read_spins'. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/gui/spin_viewer/frame.py Modified: trunk/gui/spin_viewer/frame.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/spin_viewer/frame.py?rev=21893r1=21892r2=21893view=diff == --- trunk/gui/spin_viewer/frame.py (original) +++ trunk/gui/spin_viewer/frame.py Mon Dec 9 11:50:33 2013 @@ -385,6 +385,10 @@ elif self.page_method.selection == 'new xyz': return self.page_indices['structure.read_xyz'] +# Go to the spectrum.read_spins page. +elif self.page_method.selection == 'new spectrum': +return self.page_indices['spectrum.read_spins'] + # Skip to the structure.load_spins page. elif self.page_method.selection == 'preload': return self.page_indices['structure.load_spins'] ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21896 - /trunk/test_suite/gui_tests/relax_disp.py
Author: tlinnet Date: Mon Dec 9 11:50:36 2013 New Revision: 21896 URL: http://svn.gna.org/viewcvs/relax?rev=21896view=rev Log: Further added to the GUI test for reading spins from spectrum formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/gui_tests/relax_disp.py Modified: trunk/test_suite/gui_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/relax_disp.py?rev=21896r1=21895r2=21896view=diff == --- trunk/test_suite/gui_tests/relax_disp.py (original) +++ trunk/test_suite/gui_tests/relax_disp.py Mon Dec 9 11:50:36 2013 @@ -447,6 +447,46 @@ page = self.app.gui.spin_viewer.wizard.get_page(0) page.selection = 'new spectrum' self.app.gui.spin_viewer.wizard._go_next() +page = self.app.gui.spin_viewer.wizard.get_page(self.app.gui.spin_viewer.wizard._current_page) +page.uf_args['file'].SetValue(str_to_gui(path + 'seriesTab.ser')) +self.app.gui.spin_viewer.wizard._go_next() +interpreter.flush()# Required because of the asynchronous uf call. + +# Spin loading wizard: The spin loading. +self.app.gui.spin_viewer.wizard._go_next() +interpreter.flush()# Required because of the asynchronous uf call. + +# Close the spin viewer window. +self.app.gui.spin_viewer.handler_close() + +# Flush the interpreter in preparation for the synchronous user functions of the peak list wizard. +interpreter.flush() + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 3) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 62) +self.assertEqual(cdp.mol[0].res[0].name, 'W') +self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'NE1') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 10) +self.assertEqual(cdp.mol[0].res[1].name, 'L') +self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') + +# 3rd residue. +self.assertEqual(cdp.mol[0].res[2].num, 6) +self.assertEqual(cdp.mol[0].res[2].name, 'V') +self.assertEqual(len(cdp.mol[0].res[2].spin), 1) +self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') def test_tp02_data_to_tp02(self): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21894 - /trunk/gui/spin_viewer/frame.py
Author: tlinnet Date: Mon Dec 9 11:50:34 2013 New Revision: 21894 URL: http://svn.gna.org/viewcvs/relax?rev=21894view=rev Log: Added spectrum.read_spins GUI page for reading spins from a spectrum formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/gui/spin_viewer/frame.py Modified: trunk/gui/spin_viewer/frame.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/spin_viewer/frame.py?rev=21894r1=21893r2=21894view=diff == --- trunk/gui/spin_viewer/frame.py (original) +++ trunk/gui/spin_viewer/frame.py Mon Dec 9 11:50:34 2013 @@ -223,6 +223,11 @@ self.page_indices['structure.read_xyz'] = self.wizard.add_page(page, skip_button=True) self.wizard.set_seq_next_fn(self.page_indices['structure.read_xyz'], self.wizard_page_after_structure_read) +# The spectrum.read_spins page. +page = uf_store['spectrum.read_spins'].create_page(self.wizard) +self.page_indices['spectrum.read_spins'] = self.wizard.add_page(page, skip_button=True) +self.wizard.set_seq_next_fn(self.page_indices['spectrum.read_spins'], self.wizard_page_after_sequence_read) + # The structure.load_spins page. page = uf_store['structure.load_spins'].create_page(self.wizard) self.page_indices['structure.load_spins'] = self.wizard.add_page(page) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21895 - /trunk/gui/spin_viewer/frame.py
Author: tlinnet Date: Mon Dec 9 11:50:35 2013 New Revision: 21895 URL: http://svn.gna.org/viewcvs/relax?rev=21895view=rev Log: Added radio button for reading spins from a spectrum formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/gui/spin_viewer/frame.py Modified: trunk/gui/spin_viewer/frame.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/spin_viewer/frame.py?rev=21895r1=21894r2=21895view=diff == --- trunk/gui/spin_viewer/frame.py (original) +++ trunk/gui/spin_viewer/frame.py Mon Dec 9 11:50:35 2013 @@ -514,10 +514,18 @@ self.radio_new_xyz = wx.RadioButton(self, -1, From a new XYZ structure file.) sizer_radio.Add(self.radio_new_xyz, 0, wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 0) +# Spacing. +sizer_radio.AddSpacer(20) + +# The spectrum.read_spins radio button. +self.radio_new_spectrum = wx.RadioButton(self, -1, From a spectrum formatted file.) +sizer_radio.Add(self.radio_new_spectrum, 0, wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 0) + # Bind the buttons. self.Bind(wx.EVT_RADIOBUTTON, self._on_select, self.radio_seq) self.Bind(wx.EVT_RADIOBUTTON, self._on_select, self.radio_new_pdb) self.Bind(wx.EVT_RADIOBUTTON, self._on_select, self.radio_new_xyz) +self.Bind(wx.EVT_RADIOBUTTON, self._on_select, self.radio_new_spectrum) if self.preload_flag: self.Bind(wx.EVT_RADIOBUTTON, self._on_select, self.radio_preload) @@ -551,5 +559,7 @@ self.selection = 'new pdb' elif button == self.radio_new_xyz: self.selection = 'new xyz' +elif button == self.radio_new_spectrum: +self.selection = 'new spectrum' elif self.preload_flag and button == self.radio_preload: self.selection = 'preload' ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21899 - in /trunk/lib/dispersion: ns_matrices.py ns_r1rho_3site.py
Author: bugman Date: Mon Dec 9 12:33:31 2013 New Revision: 21899 URL: http://svn.gna.org/viewcvs/relax?rev=21899view=rev Log: Added the R2eff calculating functions for the 'NS R1rho 3-site' models to the relax library. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library. Added: trunk/lib/dispersion/ns_r1rho_3site.py - copied, changed from r21888, trunk/lib/dispersion/ns_r1rho_2site.py Modified: trunk/lib/dispersion/ns_matrices.py Modified: trunk/lib/dispersion/ns_matrices.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_matrices.py?rev=21899r1=21898r2=21899view=diff == --- trunk/lib/dispersion/ns_matrices.py (original) +++ trunk/lib/dispersion/ns_matrices.py Mon Dec 9 12:33:31 2013 @@ -160,6 +160,96 @@ return temp +def rr1rho_3d_3site(matrix=None, R1=None, r1rho_prime=None, pA=None, pB=None, pC=None, wA=None, wB=None, wC=None, w1=None, k_AB=None, k_BA=None, k_BC=None, k_CB=None, k_AC=None, k_CA=None): +Definition of the 3D exchange matrix. + +@keyword matrix:The matrix to fill. +@type matrix: numpy rank-2 9D array +@keyword R1:The longitudinal, spin-lattice relaxation rate. +@type R1: float +@keyword r1rho_prime: The R1rho transverse, spin-spin relaxation rate in the absence of exchange. +@type r1rho_prime: float +@keyword pA:The population of state A. +@type pA: float +@keyword pB:The population of state B. +@type pB: float +@keyword pC:The population of state C. +@type pC: float +@keyword wA:The chemical shift offset of state A from the spin-lock. +@type wA: float +@keyword wB:The chemical shift offset of state B from the spin-lock. +@type wB: float +@keyword wC:The chemical shift offset of state C from the spin-lock. +@type wC: float +@keyword w1:The spin-lock field strength in rad/s. +@type w1: float +@keyword k_AB: The forward exchange rate from state A to state B. +@type k_AB: float +@keyword k_BA: The reverse exchange rate from state B to state A. +@type k_BA: float +@keyword k_BC: The forward exchange rate from state B to state C. +@type k_BC: float +@keyword k_CB: The reverse exchange rate from state C to state B. +@type k_CB: float +@keyword k_AC: The forward exchange rate from state A to state C. +@type k_AC: float +@keyword k_CA: The reverse exchange rate from state C to state A. +@type k_CA: float + + +# The AB auto-block. +matrix[0, 0] = -r1rho_prime - k_AB - k_AC +matrix[0, 1] = -wA +matrix[1, 0] = wA +matrix[1, 1] = -r1rho_prime - k_AB - k_AC +matrix[1, 2] = -w1 +matrix[2, 1] = w1 +matrix[2, 2] = -R1 - k_AB - k_AC + +# The AC auto-block. +matrix[3, 3] = -r1rho_prime - k_BA - k_BC +matrix[3, 4] = -wB +matrix[4, 3] = wB +matrix[4, 4] = -r1rho_prime - k_BA - k_BC +matrix[4, 5] = -w1 +matrix[5, 4] = w1 +matrix[5, 5] = -R1 - k_BA - k_BC + +# The BC auto-block. +matrix[6, 6] = -r1rho_prime - k_CA - k_CB +matrix[6, 7] = -wC +matrix[7, 6] = wC +matrix[7, 7] = -r1rho_prime - k_CA - k_CB +matrix[7, 8] = -w1 +matrix[8, 7] = w1 +matrix[8, 8] = -R1 - k_CA - k_CB + +# The AB cross-block. +matrix[3, 0] = k_AB +matrix[4, 1] = k_AB +matrix[5, 2] = k_AB +matrix[0, 3] = k_BA +matrix[1, 4] = k_BA +matrix[2, 5] = k_BA + +# The AC cross-block. +matrix[6, 0] = k_AC +matrix[7, 1] = k_AC +matrix[8, 2] = k_AC +matrix[0, 6] = k_CA +matrix[1, 7] = k_CA +matrix[2, 8] = k_CA + +# The BC cross-block. +matrix[6, 3] = k_BC +matrix[7, 4] = k_BC +matrix[8, 5] = k_BC +matrix[3, 6] = k_CB +matrix[4, 7] = k_CB +matrix[5, 8] = k_CB + + + def rr1rho_3d(R1A=None, R1=None, Rinf=None, pA=None, pB=None, wA=None, wB=None, w1=None, k_AB=None, k_BA=None): Definition of the 3D exchange matrix. Copied: trunk/lib/dispersion/ns_r1rho_3site.py (from r21888, trunk/lib/dispersion/ns_r1rho_2site.py) URL: http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_3site.py?p2=trunk/lib/dispersion/ns_r1rho_3site.pyp1=trunk/lib/dispersion/ns_r1rho_2site.pyr1=21888r2=21899rev=21899view=diff == --- trunk/lib/dispersion/ns_r1rho_2site.py (original) +++
r21900 - /trunk/gui/spin_viewer/frame.py
Author: tlinnet Date: Mon Dec 9 13:18:03 2013 New Revision: 21900 URL: http://svn.gna.org/viewcvs/relax?rev=21900view=rev Log: Fix for GUI text string for the select radio button, reading spins from a spectrum formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/gui/spin_viewer/frame.py Modified: trunk/gui/spin_viewer/frame.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/spin_viewer/frame.py?rev=21900r1=21899r2=21900view=diff == --- trunk/gui/spin_viewer/frame.py (original) +++ trunk/gui/spin_viewer/frame.py Mon Dec 9 13:18:03 2013 @@ -518,7 +518,7 @@ sizer_radio.AddSpacer(20) # The spectrum.read_spins radio button. -self.radio_new_spectrum = wx.RadioButton(self, -1, From a spectrum formatted file.) +self.radio_new_spectrum = wx.RadioButton(self, -1, From a peak list or spectrum formatted file.) sizer_radio.Add(self.radio_new_spectrum, 0, wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 0) # Bind the buttons. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21901 - /trunk/lib/dispersion/ns_r1rho_3site.py
Author: bugman Date: Mon Dec 9 13:41:09 2013 New Revision: 21901 URL: http://svn.gna.org/viewcvs/relax?rev=21901view=rev Log: Bug fix for the new 'NS R1rho 3-site' dispersion models - the Y and Z initial magnetisations were switched. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging. Modified: trunk/lib/dispersion/ns_r1rho_3site.py Modified: trunk/lib/dispersion/ns_r1rho_3site.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_3site.py?rev=21901r1=21900r2=21901view=diff == --- trunk/lib/dispersion/ns_r1rho_3site.py (original) +++ trunk/lib/dispersion/ns_r1rho_3site.py Mon Dec 9 13:41:09 2013 @@ -113,8 +113,8 @@ # The following lines rotate the magnetization previous to spin-lock into the weff frame. theta = atan(spin_lock_fields[i]/d) -M0[0] = sin(theta) -M0[1] = cos(theta) +M0[0] = sin(theta)# The A state initial X magnetisation. +M0[2] = cos(theta)# The A state initial Z magnetisation. # This matrix is a propagator that will evolve the magnetization with the matrix R. Rexpo = matrix_exponential(matrix*relax_time) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21902 - /trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/cpmg_fit_results/minimise_no_peak_shift.log
Author: bugman Date: Mon Dec 9 13:44:19 2013 New Revision: 21902 URL: http://svn.gna.org/viewcvs/relax?rev=21902view=rev Log: Added cpmg_fit results for the program modified to turn off the PEAK_SHIFT flag. These are the results which should most closely match the relax results. This is for the simulated R1rho data for the 'NS R1rho 3-site linear' model. Added: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/cpmg_fit_results/minimise_no_peak_shift.log Added: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/cpmg_fit_results/minimise_no_peak_shift.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/cpmg_fit_results/minimise_no_peak_shift.log?rev=21902view=auto == --- trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/cpmg_fit_results/minimise_no_peak_shift.log (added) +++ trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/cpmg_fit_results/minimise_no_peak_shift.log Mon Dec 9 13:44:19 2013 @@ -1,0 +1,38 @@ + Max. number of function evaluation (default): 800 +F =10368.449 +F =1445.2925 +F =33.811799 +F = 0.079456641 +F = 0.079196247 +F = 0.079196247 +F = 0.079196247 +F = 0.079196247 +F = 0.079196247 +Error: Minimization failed; INF=7 + # No model set for temperature/pressure dependencies of rate/eq. constants +# Chemical shifts are given at reference temperature: 0 C; +# No simultaneous 180 pulse is applied in MQ sequences +# Minimization is done. Minimization model is 3 +# F =0.079196246852353 DF = 0 P_lvl =0.000 + +# type temp/P val err +PA:250.8500298792762670.000 f ? ! +PB:250.0499222618908980.000 u ? ! +PC:250.1000478588328350.000 u ? ! + +# type temp/P val err +KAB: 25 500.9915496904346810.000 u ? ! +KAC: 250.0000.000 f ? ! +KBC: 25 2003.1898301663202350.000 u ? ! + +# type res nucl ord val err +CS0_A: 1N00.0000.000 f ? ! +CS0_B: 1N0 -2.9914651983104550.000 u ? ! +CS0_C: 1N08.0060335489979120.000 u ? ! + +# type res nucl/coh temp/P sfrq val err +R2_A: 1 N-R 256008.0002840379333100.000 u g ? ! +R1_A: 1 N-R 256002.0000.000 f g ? ! +R2_A: 1 N-R 258009.0002960505307160.000 u g ? ! +R1_A: 1 N-R 258003.0000.000 f g ? ! + ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21903 - /trunk/specific_analyses/relax_disp/variables.py
Author: bugman Date: Mon Dec 9 14:04:27 2013 New Revision: 21903 URL: http://svn.gna.org/viewcvs/relax?rev=21903view=rev Log: Fix for the MODEL_NS_R1RHO_3SITE_LINEAR dispersion variable. The model name was not correct. Modified: trunk/specific_analyses/relax_disp/variables.py Modified: trunk/specific_analyses/relax_disp/variables.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/variables.py?rev=21903r1=21902r2=21903view=diff == --- trunk/specific_analyses/relax_disp/variables.py (original) +++ trunk/specific_analyses/relax_disp/variables.py Mon Dec 9 14:04:27 2013 @@ -120,7 +120,7 @@ MODEL_NS_R1RHO_3SITE = 'NS R1rho 3-site' The numerical solution for the 3-site Bloch-McConnell equations for R1rho data, whereby the simplification R20A = R20B = R20C is assumed. -MODEL_NS_R1RHO_3SITE_LINEAR = 'NS R1rho 3-site' +MODEL_NS_R1RHO_3SITE_LINEAR = 'NS R1rho 3-site linear' The numerical solution for the 3-site Bloch-McConnell equations for R1rho data linearised with kAC = kCA = 0, whereby the simplification R20A = R20B = R20C is assumed. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21904 - in /trunk: docs/latex/dispersion.tex specific_analyses/relax_disp/parameters.py
Author: bugman
Date: Mon Dec 9 14:15:50 2013
New Revision: 21904
URL: http://svn.gna.org/viewcvs/relax?rev=21904view=rev
Log:
Turned off the dw dispersion parameter constraints for the 'NS R1rho 3-site'
models.
Modified:
trunk/docs/latex/dispersion.tex
trunk/specific_analyses/relax_disp/parameters.py
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21904r1=21903r2=21904view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 14:15:50 2013
@@ -1476,6 +1476,7 @@
\end{subequations}
Note that the $\dw$ and $\dwH$ constraints are not used for any of the
MMQ-type models as sign differentiation is possible.
+These constraints are also turned off for the `NS $\Ronerho$ 3-site linear'
and `NS $\Ronerho$ 3-site' models.
And that the $\pA \geqslant 0.85$ constraint is used instead of the $\pA
\geqslant 0.5$ constraint for all models which require $\pA \gg \pB$.
When not using the auto-analysis, constraints can be modified or turned off.
Modified: trunk/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameters.py?rev=21904r1=21903r2=21904view=diff
==
--- trunk/specific_analyses/relax_disp/parameters.py (original)
+++ trunk/specific_analyses/relax_disp/parameters.py Mon Dec 9 14:15:50 2013
@@ -598,7 +598,7 @@
# Chemical exchange difference (dw = 0).
elif param_name in ['dw', 'dw_AB', 'dw_AC', 'dw_BC', 'dwH', 'dwH_AB',
'dwH_AC', 'dwH_BC']:
-if not spins[0].model in MODEL_LIST_MMQ:
+if not spins[0].model in MODEL_LIST_MMQ + [MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR]:
A.append(zero_array * 0.0)
A[j][param_index] = 1.0
b.append(0.0)
___
relax (http://www.nmr-relax.com)
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relax-commits@gna.org
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r21905 - /trunk/specific_analyses/relax_disp/parameters.py
Author: bugman Date: Mon Dec 9 14:16:23 2013 New Revision: 21905 URL: http://svn.gna.org/viewcvs/relax?rev=21905view=rev Log: Missing import from the previous commit. 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=21905r1=21904r2=21905view=diff == --- trunk/specific_analyses/relax_disp/parameters.py (original) +++ trunk/specific_analyses/relax_disp/parameters.py Mon Dec 9 14:16:23 2013 @@ -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.disp_data import generate_r20_key, has_exponential_exp_type, loop_cluster, loop_exp_frq, return_value_from_frq_index -from specific_analyses.relax_disp.variables import MODEL_LIST_MMQ, MODEL_M61B, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR +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 def assemble_param_vector(spins=None, key=None, sim_index=None): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21906 - /trunk/auto_analyses/relax_disp.py
Author: bugman Date: Mon Dec 9 14:20:10 2013 New Revision: 21906 URL: http://svn.gna.org/viewcvs/relax?rev=21906view=rev Log: Added the 'NS R1rho 3-site' models to the dispersion auto-analysis. This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis. Modified: trunk/auto_analyses/relax_disp.py Modified: trunk/auto_analyses/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=21906r1=21905r2=21906view=diff == --- trunk/auto_analyses/relax_disp.py (original) +++ trunk/auto_analyses/relax_disp.py Mon Dec 9 14:20:10 2013 @@ -36,7 +36,7 @@ from pipe_control.pipes import has_pipe from prompt.interpreter import Interpreter from specific_analyses.relax_disp.disp_data import has_exponential_exp_type, has_cpmg_exp_type, has_fixed_time_exp_type, has_r1rho_exp_type, loop_frq -from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC, MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_LIST_NUMERIC, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 +from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC, MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_LIST_NUMERIC, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 from status import Status; status = Status() @@ -250,6 +250,14 @@ nested_pipe = MODEL_NS_MMQ_3SITE_LINEAR elif MODEL_NS_MMQ_2SITE in self.models: nested_pipe = MODEL_NS_MMQ_2SITE +if model == MODEL_NS_R1RHO_3SITE_LINEAR and MODEL_NS_R1RHO_2SITE in self.models: +nested_pipe = MODEL_NS_R1RHO_2SITE +if model == MODEL_NS_R1RHO_3SITE: +if MODEL_NS_R1RHO_3SITE_LINEAR in self.models: +nested_pipe = MODEL_NS_R1RHO_3SITE_LINEAR +elif MODEL_NS_R1RHO_2SITE in self.models: +nested_pipe = MODEL_NS_R1RHO_2SITE + # Using the analytic solution. analytic = False @@ -525,12 +533,12 @@ #self.interpreter.grace.write(x_data_type='res_num', y_data_type='r2', file='r1rho0.agr', dir=path, force=True) # The pA, pB, and pC parameters. -if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61B, MODEL_MMQ_CR72, 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, MODEL_NS_MMQ_2SITE, MODEL_NS_R1RHO_2SITE, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: +if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61B, MODEL_MMQ_CR72, 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, MODEL_NS_MMQ_2SITE, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: self.interpreter.value.write(param='pA', file='pA.out', dir=path, force=True) self.interpreter.value.write(param='pB', file='pB.out', dir=path, force=True) self.interpreter.grace.write(x_data_type='res_num', y_data_type='pA', file='pA.agr', dir=path, force=True) self.interpreter.grace.write(x_data_type='res_num', y_data_type='pB', file='pB.agr', dir=path, force=True) -if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: +if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]: self.interpreter.value.write(param='pC', file='pC.out', dir=path, force=True) self.interpreter.grace.write(x_data_type='res_num', y_data_type='pC', file='pC.agr', dir=path, force=True) @@ -550,7 +558,7 @@ if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61B, MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR,
r21907 - /trunk/gui/analyses/auto_relax_disp.py
Author: bugman
Date: Mon Dec 9 14:25:20 2013
New Revision: 21907
URL: http://svn.gna.org/viewcvs/relax?rev=21907view=rev
Log:
Added the 'NS R1rho 3-site' models to the GUI model list.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
Modified:
trunk/gui/analyses/auto_relax_disp.py
Modified: trunk/gui/analyses/auto_relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/analyses/auto_relax_disp.py?rev=21907r1=21906r2=21907view=diff
==
--- trunk/gui/analyses/auto_relax_disp.py (original)
+++ trunk/gui/analyses/auto_relax_disp.py Mon Dec 9 14:25:20 2013
@@ -48,7 +48,7 @@
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
from pipe_control.pipes import has_bundle, has_pipe
from specific_analyses.relax_disp.disp_data import has_cpmg_exp_type,
has_r1rho_exp_type
-from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_R1RHO,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_CR72,
MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03,
MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_R1RHO,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_CR72,
MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
from status import Status; status = Status()
@@ -731,6 +731,8 @@
MODEL_TAP03,
MODEL_MP05,
MODEL_NS_R1RHO_2SITE,
+MODEL_NS_R1RHO_3SITE_LINEAR,
+MODEL_NS_R1RHO_3SITE,
None,
MODEL_MMQ_CR72,
MODEL_NS_MMQ_2SITE,
@@ -761,6 +763,8 @@
{%s, ..., pA, %s, %s} % (r1rho_prime, dw, kex),
{%s, ..., pA, %s, %s} % (r1rho_prime, dw, kex),
{%s, ..., pA, %s, %s} % (r1rho_prime, dw, kex),
+{%s, ..., pA, %s, %s, pB, %s, %s} % (r1rho_prime, dw_AB, kAB, dw_BC,
kBC),
+{%s, ..., pA, %s, %s, pB, %s, %s, %s} % (r1rho_prime, dw_AB, kAB,
dw_BC, kBC, kAC),
None,
{%s, ..., pA, %s, %s, %s} % (r2, dw, dwH, kex),
{%s, ..., pA, %s, %s, %s} % (r2, dw, dwH, kex),
@@ -791,6 +795,8 @@
The Trott, Abergel and Palmer (2003) off-resonance 2-site equation
for all time scales.,
The Miloushev and Palmer (2005) off-resonance 2-site equation for all
time scales.,
The 2-site numerical solution using 3D magnetisation vectors.,
+The 3-site linearised numerical solution using 3D magnetisation
vectors.,
+The 3-site numerical solution using 3D magnetisation vectors.,
None,
The CR72 2-site model extended to MMQ CPMG data by Korzhnev et al.,
2004.,
The 2-site numerical solution of Korzhnev et al. (2004) from
multi-quantum CPMG data.,
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r21908 - in /trunk: docs/latex/dispersion.tex specific_analyses/relax_disp/parameters.py
Author: bugman
Date: Mon Dec 9 14:33:05 2013
New Revision: 21908
URL: http://svn.gna.org/viewcvs/relax?rev=21908view=rev
Log:
Removed the pC = pB constraint from the 3-site dispersion models.
This is important for the linear models where a violation of this constraint is
reasonable. This
has been replaced by the pC = pA constraint.
Modified:
trunk/docs/latex/dispersion.tex
trunk/specific_analyses/relax_disp/parameters.py
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21908r1=21907r2=21908view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 14:33:05 2013
@@ -1460,10 +1460,9 @@
\dwHAB \geqslant 0, \\
\dwHBC \geqslant 0, \\
\pA\dw^2 \geqslant 0, \\
-\pA \geqslant 0, \\
-\pB \geqslant 0, \\
-\pC \geqslant 0, \\
-\pC \leqslant \pB \leqslant \pA \leqslant 1, \\
+0 \leqslant \pA \leqslant 1, \\
+0 \leqslant \pB \leqslant \pA, \\
+0 \leqslant \pC \leqslant \pA, \\
\pA \geqslant 0.85 \quad (\textrm{the skewed condition, } \pA \gg \pB), \\
0 \leqslant \kex \leqslant 2e^6, \\
0 \leqslant \kexAB \leqslant 2e^6, \\
Modified: trunk/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameters.py?rev=21908r1=21907r2=21908view=diff
==
--- trunk/specific_analyses/relax_disp/parameters.py (original)
+++ trunk/specific_analyses/relax_disp/parameters.py Mon Dec 9 14:33:05 2013
@@ -638,11 +638,11 @@
b.append(-1.0 / scaling_matrix[param_index, param_index])
j += 1
-# Then the pB = pC constraint (rearranged as pA + 2pB =
1).
+# Then the pA = pC constraint.
A.append(zero_array * 0.0)
A[j][param_index2] = 1.0
-A[j][param_index] = 2.0
-b.append(1.0 / scaling_matrix[param_index, param_index])
+A[j][param_index] = -1.0
+b.append(0.0)
j += 1
break
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r21909 - in /trunk/docs/latex: dispersion.tex dispersion_models.tex dispersion_software.tex relax.tex
Author: bugman
Date: Mon Dec 9 16:05:35 2013
New Revision: 21909
URL: http://svn.gna.org/viewcvs/relax?rev=21909view=rev
Log:
Added the 'NS R1rho 3-site' models to the relax user manual.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
Modified:
trunk/docs/latex/dispersion.tex
trunk/docs/latex/dispersion_models.tex
trunk/docs/latex/dispersion_software.tex
trunk/docs/latex/relax.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21909r1=21908r2=21909view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 16:05:35 2013
@@ -127,6 +127,8 @@
\begin{description}
\item[`NS R1rho 2-site':]\index{relaxation dispersion!NS R1rho 2-site model}
The model for 2-site exchange using 3D magnetisation vectors. It has the
parameters $\{\Ronerhoprime, \dots, \pA, \dw, \kex\}$. See Section~\ref{sect:
dispersion: NS R1rho 2-site model} on page~\pageref{sect: dispersion: NS R1rho
2-site model}.
+\item[`NS $\Ronerho$ 3-site linear':]\index{relaxation dispersion!NS R1rho
3-site linear model} The model for 3-site exchange linearised with
$\kAC=\kCA=0$ whereby the simplification $\RonerhoprimeA = \RonerhoprimeB =
\RonerhoprimeC$ is assumed. It has the parameters \{$\Ronerhoprime$, $\dots$,
$\pA$, $\pB$, $\dwAB$, $\dwBC$, $\kexAB$, $\kexBC$\}. See Section~\ref{sect:
dispersion: NS R1rho 3-site linear model} on page~\pageref{sect: dispersion: NS
R1rho 3-site linear model}.
+\item[`NS $\Ronerho$ 3-site':]\index{relaxation dispersion!NS R1rho 3-site
model} The model for 3-site exchange whereby the simplification
$\RonerhoprimeA = \RonerhoprimeB = \RonerhoprimeC$ is assumed. It has the
parameters \{$\Ronerhoprime$, $\dots$, $\pA$, $\pB$, $\dwAB$, $\dwBC$,
$\kexAB$, $\kexBC$, $\kexAC$\}. See Section~\ref{sect: dispersion: NS R1rho
3-site model} on page~\pageref{sect: dispersion: NS R1rho 3-site model}.
\end{description}
@@ -1128,6 +1130,143 @@
where $\delta_{A,B}$ is defined in Equations~\ref{eq: deltaA} and~\ref{eq:
deltaB}.
+% NS R1rho 3-site model.
+%~~~
+
+\subsection{The NS 3-site $\Ronerho$ model}
+\label{sect: dispersion: NS R1rho 3-site model}
+\index{relaxation dispersion!NS R1rho 3-site model|textbf}
+
+This is the numerical model for 3-site exchange using 3D magnetisation vectors.
+It is selected by setting the model to `NS R1rho 3-site'.
+The constraints $\pA \pB$ and $\pA \pC$ is used to decrease the size of
the optimisation space, as both sides of the limit are mirror image spaces.
+
+For this model, as for the 2-site model above, the equations from
\citet{Korzhnev05a} have been used.
+These have been however rearranged to match the notation in
\citet{PalmerMassi06}.
+The $\Ronerho$ value for state A magnetisation is defined as
+\begin{equation}
+\Ronerho = - \frac{1}{T_\textrm{relax}} \cdot \ln \left( M_0^T \cdot e^{R
\cdot T_\textrm{relax}} \cdot M_0 \right),
+\end{equation}
+
+where
+\begin{align}
+M_0= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0
\\ 0 \\ 0 \\ 0 \end{pmatrix}, \\
+\theta = \arctan \left( \frac{\omegaone}{\aveoffset} \right).
+\end{align}
+
+This assumes that the starting magnetisation has an X and Z component only for
the A state.
+The relaxation evolution matrix is defined as
+\begin{align}
+R = \begin{pmatrix}
+ -\RonerhoprimeA-\kAB-\kAC -\delta_A 0
\cdots \\
+ \delta_A -\RonerhoprimeA-\kAB-\kAC -\omegaone
\cdots \\
+ 0 \omegaone
-\RoneA-\kAB-\kAC \cdots \\
+ \vdots \vdots \vdots
\ddots \\
+ \end{pmatrix} \nonumber \\
+ + \begin{pmatrix}
+ \ddots \vdots \vdots
\vdots \iddots \\
+ \cdots -\RonerhoprimeB-\kBA-\kBC -\delta_B 0
\cdots \\
+ \cdots \delta_B -\RonerhoprimeB-\kBA-\kBC
-\omegaone \cdots \\
+ \cdots 0 \omegaone
-\RoneB-\kBA-\kBC \cdots \\
+ \iddots \vdots \vdots
\vdots \ddots \\
+ \end{pmatrix} \nonumber \\
+ + \begin{pmatrix}
+ \ddots \vdots \vdots
\vdots \\
+ \cdots -\RonerhoprimeC-\kCA-\kCB -\delta_C 0
\\
+ \cdots \delta_C -\RonerhoprimeC-\kCA-\kCB
-\omegaone \\
+
r21910 - in /trunk: docs/latex/dispersion.tex lib/dispersion/ns_matrices.py
Author: bugman
Date: Mon Dec 9 16:33:33 2013
New Revision: 21910
URL: http://svn.gna.org/viewcvs/relax?rev=21910view=rev
Log:
Transposed some of the 'NS R1rho 3-site' model evolution matrix elements.
These now match the 'NS R1rho 2-site' model.
Modified:
trunk/docs/latex/dispersion.tex
trunk/lib/dispersion/ns_matrices.py
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21910r1=21909r2=21910view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 16:33:33 2013
@@ -1177,31 +1177,31 @@
\cdots 0 \omegaone
-\RoneC-\kCA-\kCB \\
\end{pmatrix} \nonumber \\
+ \begin{pmatrix}
- \kAB 00\cdots
\\
-\ddots0\kAB 0\cdots
\\
- 00\kAB \cdots
\\
- \kBA 00 \\
- 0\kBA 0 \ddots\cdots\\
- 00\kBA\\
+ \kBA 00\cdots
\\
+\ddots0\kBA 0\cdots
\\
+ 00\kBA \cdots
\\
+ \kAB 00 \\
+ 0\kAB 0 \ddots\cdots\\
+ 00\kAB\\
\vdots \vdots \vdots\vdots\ddots
\\
\end{pmatrix} \nonumber \\
+ \begin{pmatrix}
- \cdots \kAC 00 \\
-\ddots\cdots 0\kAC 0 \\
- \cdots 00\kAC \\
+ \cdots \kCA 00 \\
+\ddots\cdots 0\kCA 0 \\
+ \cdots 00\kCA \\
\vdots \vdots \vdots \ddots \vdots \vdots \vdots
\\
- \kCA 00\cdots \\
- 0\kCA 0\cdots\ddots\\
- 00\kCA \cdots \\
+ \kAC 00\cdots \\
+ 0\kAC 0\cdots\ddots\\
+ 00\kAC \cdots \\
\end{pmatrix} \nonumber \\
+ \begin{pmatrix}
\ddots\vdots\vdots \vdots \vdots
\\
- \kBC 00 \\
- \cdots\ddots0\kBC 0 \\
- 00\kBC \\
- \cdots \kCB 00 \\
- \cdots 0\kCB 0 \ddots\\
- \cdots 00\kCB\\
+ \kCB 00 \\
+ \cdots\ddots0\kCB 0 \\
+ 00\kCB \\
+ \cdots \kBC 00 \\
+ \cdots 0\kBC 0 \ddots\\
+ \cdots 00\kBC\\
\end{pmatrix},
\end{align}
@@ -1244,22 +1244,22 @@
\cdots 0 \omegaone -\RoneC-\kCB
\\
\end{pmatrix} \nonumber \\
+ \begin{pmatrix}
- \kAB 00\cdots
\\
-\ddots0\kAB 0\cdots
\\
- 00\kAB \cdots
\\
- \kBA 00 \\
- 0\kBA 0 \ddots\cdots\\
- 00\kBA\\
+ \kBA 00\cdots
\\
+\ddots0\kBA 0\cdots
\\
+ 00\kBA \cdots
\\
+ \kAB 00 \\
+ 0\kAB 0 \ddots\cdots\\
+ 00\kAB\\
\vdots \vdots \vdots\vdots\ddots
\\
r21911 - in /trunk: docs/latex/dispersion.tex docs/latex/relax.tex lib/dispersion/ns_r1rho_3site.py
Author: bugman
Date: Mon Dec 9 16:57:34 2013
New Revision: 21911
URL: http://svn.gna.org/viewcvs/relax?rev=21911view=rev
Log:
Last fixes for the 'NS R1rho 3-site' dispersion models.
These now behave identically to the cpmg_fit program with the PEAK_SHIFT flag
disabled. The tilt
angle for the initial magnetisation is no longer that for the average offset
but that of state A.
Modified:
trunk/docs/latex/dispersion.tex
trunk/docs/latex/relax.tex
trunk/lib/dispersion/ns_r1rho_3site.py
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21911r1=21910r2=21911view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 16:57:34 2013
@@ -1151,7 +1151,7 @@
where
\begin{align}
M_0= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0
\\ 0 \\ 0 \\ 0 \end{pmatrix}, \\
-\theta = \arctan \left( \frac{\omegaone}{\aveoffset} \right).
+\theta = \arctan \left( \frac{\omegaone}{\offsetA} \right).
\end{align}
This assumes that the starting magnetisation has an X and Z component only for
the A state.
Modified: trunk/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=21911r1=21910r2=21911view=diff
==
--- trunk/docs/latex/relax.tex (original)
+++ trunk/docs/latex/relax.tex Mon Dec 9 16:57:34 2013
@@ -135,6 +135,9 @@
\newcommand{\KL}{\Delta_{\scriptscriptstyle \text{K-L}}}
\newcommand{\aveoffset}{\bar\Omega}
+\newcommand{\offsetA}{\Omega_\textrm{A}}
+\newcommand{\offsetB}{\Omega_\textrm{B}}
+\newcommand{\offsetC}{\Omega_\textrm{C}}
\newcommand{\aveomega}{\bar\omega}
\newcommand{\dw}{\Delta\omega}
\newcommand{\dwAB}{\Delta\omega_\textrm{AB}}
Modified: trunk/lib/dispersion/ns_r1rho_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_3site.py?rev=21911r1=21910r2=21911view=diff
==
--- trunk/lib/dispersion/ns_r1rho_3site.py (original)
+++ trunk/lib/dispersion/ns_r1rho_3site.py Mon Dec 9 16:57:34 2013
@@ -112,7 +112,7 @@
rr1rho_3d_3site(matrix=matrix, R1=r1, r1rho_prime=r1rho_prime, pA=pA,
pB=pB, pC=pC, wA=dA, wB=dB, wC=dC, w1=spin_lock_fields[i], k_AB=k_AB,
k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA)
# The following lines rotate the magnetization previous to spin-lock
into the weff frame.
-theta = atan(spin_lock_fields[i]/d)
+theta = atan(spin_lock_fields[i]/dA)
M0[0] = sin(theta)# The A state initial X magnetisation.
M0[2] = cos(theta)# The A state initial Z magnetisation.
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r21914 - /trunk/docs/latex/dispersion_params.tex
Author: bugman
Date: Mon Dec 9 17:19:26 2013
New Revision: 21914
URL: http://svn.gna.org/viewcvs/relax?rev=21914view=rev
Log:
Added the Omega_A,B,C resonance offset parameter definitions to the dispersion
chapter of the manual.
Modified:
trunk/docs/latex/dispersion_params.tex
Modified: trunk/docs/latex/dispersion_params.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion_params.tex?rev=21914r1=21913r2=21914view=diff
==
--- trunk/docs/latex/dispersion_params.tex (original)
+++ trunk/docs/latex/dispersion_params.tex Mon Dec 9 17:19:26 2013
@@ -32,6 +32,9 @@
$\RtwozeroB$- $\Rtwo$ relaxation rate
for state B in the absence of exchange rad.s$^{-1}$ \\
$\Ronerhoprime$ - $\Ronerho$ relaxation
rate in the absence of exchange rad.s$^{-1}$ \\
$\aveoffset$$\aveomega - \omegarf$ The average resonance
offset in the rotating frame rad.s$^{-1}$ \\
+$\offsetA$ $\omegaA - \omegarf$The resonance offset in
the rotating frame for state A rad.s$^{-1}$ \\
+$\offsetB$ $\omegaB - \omegarf$The resonance offset in
the rotating frame for state B rad.s$^{-1}$ \\
+$\offsetC$ $\omegaC - \omegarf$The resonance offset in
the rotating frame for state C rad.s$^{-1}$ \\
$\omegaA$ - The Larmor frequency of
the spin in state Arad.s$^{-1}$ \\
$\omegaB$ - The Larmor frequency of
the spin in state Brad.s$^{-1}$ \\
$\omegaC$ - The Larmor frequency of
the spin in state Crad.s$^{-1}$ \\
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r21916 - in /trunk: docs/latex/ lib/dispersion/ target_functions/ test_suite/system_tests/
Author: bugman
Date: Mon Dec 9 17:30:16 2013
New Revision: 21916
URL: http://svn.gna.org/viewcvs/relax?rev=21916view=rev
Log:
Modified the 'NS R1rho 2-site' dispersion model to match the 'NS R1rho 3-site'
models.
The 6D evolution matrix indices have been rearranged to match the 9D matrix
indices. The tilt angle
for the initial magnetisation is no longer that for the average offset but that
of state A, as was
changed for the 'NS R1rho 3-site' models earlier (r21911). The system test was
therefore updated
for the slightly different behaviour.
Modified:
trunk/docs/latex/dispersion.tex
trunk/lib/dispersion/ns_matrices.py
trunk/lib/dispersion/ns_r1rho_2site.py
trunk/target_functions/relax_disp.py
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21916r1=21915r2=21916view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Mon Dec 9 17:30:16 2013
@@ -,20 +,20 @@
where
\begin{align}
-M_0= \begin{pmatrix} \sin{\theta} \\ 0 \\ 0 \\ 0 \\ \cos{\theta} \\ 0
\end{pmatrix}, \\
-\theta = \arctan \left( \frac{\omegaone}{\aveoffset} \right).
+M_0= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0
\end{pmatrix}, \\
+\theta = \arctan \left( \frac{\omegaone}{\offsetA} \right).
\end{align}
The relaxation evolution matrix is defined as
\begin{equation}
-R = -\begin{pmatrix}
- \Ronerhoprime+\kAB -\kBA \delta_A0
0 0 \\
- -\kAB \Ronerhoprime+\kBA 0
\delta_B0 0 \\
- -\delta_A 0 \Ronerhoprime+\kAB
-\kBA \omegaone 0 \\
- 0 -\delta_B -\kAB
\Ronerhoprime+\kBA 0 \omegaone \\
- 0 0 -\omegaone 0
\Rone+\kAB -\kBA \\
- 0 0 0
-\omegaone -\kAB \Rone+\kBA \\
- \end{pmatrix},
+R = \begin{pmatrix}
+ -\Ronerhoprime-\kAB -\delta_A0\kBA
00 \\
+ \delta_A -\Ronerhoprime-\kAB -\omegaone 0
\kBA 0 \\
+ 0\omegaone-\Rone-\kAB 0
0\kBA \\
+ \kAB 00
-\Ronerhoprime-\kBA -\delta_B0 \\
+ 0\kAB 0\delta_B
-\Ronerhoprime-\kBA -\omegaone \\
+ 00\kAB 0
\omegaone-\Rone-\kBA \\
+\end{pmatrix},
\end{equation}
where $\delta_{A,B}$ is defined in Equations~\ref{eq: deltaA} and~\ref{eq:
deltaB}.
Modified: trunk/lib/dispersion/ns_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_matrices.py?rev=21916r1=21915r2=21916view=diff
==
--- trunk/lib/dispersion/ns_matrices.py (original)
+++ trunk/lib/dispersion/ns_matrices.py Mon Dec 9 17:30:16 2013
@@ -249,43 +249,56 @@
matrix[8, 5] = k_BC
-def rr1rho_3d(R1A=None, R1=None, Rinf=None, pA=None, pB=None, wA=None,
wB=None, w1=None, k_AB=None, k_BA=None):
+def rr1rho_3d(matrix=None, R1=None, r1rho_prime=None, pA=None, pB=None,
wA=None, wB=None, w1=None, k_AB=None, k_BA=None):
Definition of the 3D exchange matrix.
This code originates from the funNumrho.m file from the Skrynikov
Tollinger code (the sim_all.tar file
https://gna.org/support/download.php?file_id=18404 attached to
https://gna.org/task/?7712#comment5).
-@keyword R1:The longitudinal, spin-lattice relaxation rate.
-@type R1: float
-@keyword Rinf: The R1rho transverse, spin-spin relaxation rate in the
absence of exchange.
-@type Rinf: float
-@keyword pA:The population of state A.
-@type pA: float
-@keyword pB:The population of state B.
-@type pB: float
-@keyword wA:The chemical shift offset of state A from the spin-lock.
-@type wA: float
-@keyword wB:The chemical shift offset of state A from the spin-lock.
-@type wB: float
-@keyword w1:The spin-lock field strength in rad/s.
-@type w1: float
-@keyword k_AB: The forward exchange rate from state A to state B.
-@type k_AB: float
-@keyword k_BA: The reverse exchange rate from state B to state A.
-@type k_BA: float
-@return:The relaxation matrix.
-@rtype:
r21917 - /trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/
Author: bugman Date: Mon Dec 9 17:33:28 2013 New Revision: 21917 URL: http://svn.gna.org/viewcvs/relax?rev=21917view=rev Log: Updated the relax results for the Fyn SH3 R1rho dispersion data. This is for the recent changes to the 'NS R1rho 2-site' dispersion model. Modified: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.agr.bz2 trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.bz2 trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.log.bz2 Modified: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.agr.bz2 URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.agr.bz2?rev=21917r1=21916r2=21917view=diff == Binary files - no diff available. Modified: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.bz2 URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.bz2?rev=21917r1=21916r2=21917view=diff == Binary files - no diff available. Modified: trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.log.bz2 URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Fyn_SH3_R1rho/relax_results/solution_ns_r1rho_2site.log.bz2?rev=21917r1=21916r2=21917view=diff == Binary files - no diff available. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21918 - in /trunk/test_suite/system_tests: relax_disp.py scripts/relax_disp/ns_r1rho_3site_linear.py
Author: bugman
Date: Mon Dec 9 17:37:16 2013
New Revision: 21918
URL: http://svn.gna.org/viewcvs/relax?rev=21918view=rev
Log:
Updated the Relax_disp.test_ns_r1rho_3site_linear system test so it now passes.
The chi-squared value is not exactly zero as there are numerical differences
between relax and
cpmg_fit due to different approaches being used.
Modified:
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21918r1=21917r2=21918view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 17:37:16 2013
@@ -2447,7 +2447,7 @@
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_r1rho_3site_linear.py')
# Check the chi-squared value.
-self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 0.0, 3)
+self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2,
0.030959849811015544, 3)
def test_r2eff_read(self):
Modified:
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py?rev=21918r1=21917r2=21918view=diff
==
--- trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
Mon Dec 9 17:37:16 2013
@@ -96,33 +96,33 @@
relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
# Change the model.
-relax_disp.select_model('NS R1rho 3-site')
+relax_disp.select_model('NS R1rho 3-site linear')
# The R20 keys.
r20_600_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=600e6)
r20_800_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
-# Manually set the parameter values.
+# Manually set the parameter values to the cpmg_fit solution with the
PEAK_SHIFT flag turned off.
spin = cdp.mol[0].res[0].spin[0]
spin.r2 = {
-r20_600_key: 8.0,
-r20_800_key: 9.0,
+r20_600_key: 8.000284037933310,
+r20_800_key: 9.000296050530716,
}
-spin.pA = 0.85
-spin.pB = 0.05
-spin.pC = 0.10
-spin.kAB = 500.0
-spin.kAC = 0.0
-spin.kBC = 2000.0
-spin.dw_AB = -3.0
-spin.dw_AC = 8.0
-spin.dw_BC = 11.0
+spin.pA = 0.850029879276267
+spin.pB = 0.049922261890898
+spin.pC = 0.100047858832835
+spin.kex_AB = 500.991549690434681
+spin.kex_AC = 0.0
+spin.kex_BC = 2003.189830166320235
+spin.dw_AB = -2.991465198310455
+spin.dw_AC = 8.006033548997912
+spin.dw_BC = spin.dw_AC - spin.dw_AB
# Calculate.
calc()
-# Plot the dispersion curves.
-relax_disp.plot_disp_curves(dir=ds.tmpdir, num_points=100, extend=0,
force=True)
+# Plot the dispersion curves (commented out as it is currently too slow).
+#relax_disp.plot_disp_curves(dir=ds.tmpdir, num_points=100, extend=0,
force=True)
# Save the results.
state.save('state', dir=ds.tmpdir, compress_type=1, force=True)
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r21920 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet
Date: Mon Dec 9 17:49:49 2013
New Revision: 21920
URL: http://svn.gna.org/viewcvs/relax?rev=21920view=rev
Log:
Added system test for the analysis of optimisation of the Kjaergaard et al.,
2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL'
model.
Work in progress for Support Request #3083,
(https://gna.org/support/index.php?3083) - Addition of Data-set for R1rho
analysis.
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21920r1=21919r2=21920view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 17:49:49 2013
@@ -2450,6 +2450,137 @@
self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2,
0.030959849811015544, 3)
+def test_r1rho_kjaergaard(self):
+Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
+
+This uses the data from Kjaergaard's paper at U{DOI:
10.1021/bi4001062http://dx.doi.org/10.1021/bi4001062}.
+
+
+
+# The path to the data files.
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'
+
+# Set pipe name, bundle and type.
+pipe_name = 'base pipe'
+pipe_bundle = 'relax_disp'
+pipe_type= 'relax_disp'
+
+# Create the data pipe.
+self.interpreter.pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
pipe_type=pipe_type)
+
+# Read the spins.
+self.interpreter.spectrum.read_spins(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
+
+# Test some of the sequence.
+self.assertEqual(len(cdp.mol), 1)
+self.assertEqual(cdp.mol[0].name, None)
+self.assertEqual(len(cdp.mol[0].res), 48)
+
+# Name the isotope for field strength scaling.
+self.interpreter.spin.isotope(isotope='15N')
+
+# Set number of experiments to be used.
+NR_exp = -1
+
+# Load the experiments settings file.
+expfile = open(data_path+sep+'exp_parameters_sort.txt','r')
+expfileslines = expfile.readlines()[:NR_exp]
+expfile.close()
+
+# In MHz
+yOBS = 81.050
+# In ppm
+yCAR = 118.078
+centerPPM_N15 = yCAR
+
+## Read the chemical shift data.
+self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
+
+# Test the chemical shift data.
+cs = [122.223, 122.162, 114.250, 125.852, 118.626, 117.449, 119.999,
122.610, 118.602, 118.291, 115.393,
+121.288, 117.448, 116.378, 116.316, 117.263, 122.211, 118.748,
118.103, 119.421, 119.317, 119.386, 117.279,
+122.103, 120.038, 116.698, 111.811, 118.639, 118.285, 121.318,
117.770, 119.948, 119.759, 118.314, 118.160,
+121.442, 118.714, 113.080, 125.706, 119.183, 120.966, 122.361,
126.675, 117.069, 120.875, 109.372, 119.811, 126.048]
+
+i = 0
+for spin, spin_id in spin_loop(return_id=True):
+print spin.name, spin.num, spin_id, spin.chemical_shift, cs[i]
+# Check the chemical shift.
+self.assertEqual(spin.chemical_shift, cs[i])
+
+# Increment the index.
+i += 1
+
+# The lock power to field, has been found in an calibration experiment.
+spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': 800.5,
'43': 984.0, '46': 1341.11, '48': 1648.5}
+
+# Apply spectra settings.
+for i in range(len(expfileslines)):
+line=expfileslines[i]
+if line[0] == #:
+continue
+else:
+# DIRN I deltadof2 dpwr2slock ncyc trim ss sfrq
+DIRN = line.split()[0]
+I = int(line.split()[1])
+deltadof2 = line.split()[2]
+dpwr2slock = line.split()[3]
+ncyc = int(line.split()[4])
+trim = float(line.split()[5])
+ss = int(line.split()[6])
+set_sfrq = float(line.split()[7])
+apod_rmsd = float(line.split()[8])
+spin_lock_field_strength =
spin_lock_field_strengths_Hz[dpwr2slock]
+
+# Calculate spin_lock time
+time_sl = 2*ncyc*trim
+
+# Define file name for peak list.
+FNAME = %s_%s_%s_%s_max_standard.ser%(I, deltadof2,
dpwr2slock, ncyc)
+sp_id = %s_%s_%s_%s%(I, deltadof2, dpwr2slock, ncyc)
+
+# Load the peak intensities.
+self.interpreter.spectrum.read_intensities(file=FNAME,
dir=data_path+sep+'peak_lists', spectrum_id=sp_id, int_method='height')
+
+
r21919 - in /trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013: exp_parameters.txt exp_parameters_sort.txt
Author: tlinnet Date: Mon Dec 9 17:49:35 2013 New Revision: 21919 URL: http://svn.gna.org/viewcvs/relax?rev=21919view=rev Log: Added the RMSD determined via showApod for the 69 experiments. Work in progress for Support Request #3083, (https://gna.org/support/index.php?3083) - Addition of Data-set for R1rho analysis. Modified: trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_parameters.txt trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_parameters_sort.txt [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_parameters.txt URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_parameters.txt?rev=21919r1=21918r2=21919view=diff Modified: trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_parameters_sort.txt URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/exp_parameters_sort.txt?rev=21919r1=21918r2=21919view=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
r21921 - /trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/
Author: tlinnet
Date: Mon Dec 9 17:49:50 2013
New Revision: 21921
URL: http://svn.gna.org/viewcvs/relax?rev=21921view=rev
Log:
Modified analysis script for example data of R1rho.
Work in progress for Support Request #3083,
(https://gna.org/support/index.php?3083) - Addition of Data-set for R1rho
analysis.
Modified:
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
Modified:
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py?rev=21921r1=21920r2=21921view=diff
==
---
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
(original)
+++
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_1_ini.py
Mon Dec 9 17:49:50 2013
@@ -11,10 +11,13 @@
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
# Create the spins
-script(file='relax_2_spins.py', dir=None)
+spectrum.read_spins('peaks_corr_final.list')
# Name the isotope for field strength scaling.
spin.isotope(isotope='15N')
+
+## Read the chemical shift data.
+chemical_shift.read(file='peaks_corr_final.list', dir=None)
# Set the spectra experimental properties/settings.
script(file='r1rho_3_spectra_settings.py', dir=None)
Modified:
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py?rev=21921r1=21920r2=21921view=diff
==
---
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
(original)
+++
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_3_spectra_settings.py
Mon Dec 9 17:49:50 2013
@@ -23,9 +23,6 @@
#gyro15N = 2.7126E7
writefile = open('omega_rf_ppm.txt','w')
-
-## Read the chemical shift data.
-chemical_shift.read(file='peaks_corr_final.list', dir=None)
for i in range(len(expfileslines)):
line=expfileslines[i]
Modified:
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py?rev=21921r1=21920r2=21921view=diff
==
---
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
(original)
+++
trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/r1rho_4_run.py
Mon Dec 9 17:49:50 2013
@@ -8,8 +8,12 @@
import os
from auto_analyses.relax_disp import Relax_disp
+# Setting variables for pipe names.
+pipe_name = 'base pipe'
+pipe_bundle = 'relax_disp'
+
# The dispersion models.
-MODELS = ['R2eff', 'DPL94']
+MODELS = ['R2eff', 'No Rex', 'DPL94']
# The grid search size (the number of increments per dimension).
GRID_INC = 4
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
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r21922 - in /trunk/test_suite/shared_data/dispersion/ns_r1rho_3site: ./ cpmg_fit_results/ relax_results/
Author: bugman Date: Mon Dec 9 18:00:12 2013 New Revision: 21922 URL: http://svn.gna.org/viewcvs/relax?rev=21922view=rev Log: Created synthetic R1rho dispersion data for the 'NS R1rho 3-site' model. This is a simple modification of the data for the 'NS R1rho 3-site linear' model. The k_AC parameter was simply changed from 0 to 1000. The cpmg_fit software was used to create the data. Both cpmg_fit and relax results have been updated to the new model. Added: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/ - copied from r21916, trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/ Modified: trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_5500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_6000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/600_MHz_75.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_5500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_6000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/800_MHz_75.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/all.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/back_calculate.cpmg_fit trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_100.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_1000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_1500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_200.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_2000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_2500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_300.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_3000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_3500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_400.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_4000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_4500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_50.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_500.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_5000.res trunk/test_suite/shared_data/dispersion/ns_r1rho_3site/cpmg_fit_results/600_MHz_5500.res
r21923 - in /trunk/test_suite/system_tests: relax_disp.py scripts/relax_disp/ns_r1rho_3site.py
Author: bugman
Date: Mon Dec 9 18:08:58 2013
New Revision: 21923
URL: http://svn.gna.org/viewcvs/relax?rev=21923view=rev
Log:
Created the new Relax_disp.test_ns_r1rho_3site system test.
This was copied from the Relax_disp.test_ns_r1rho_3site_linear test and
modified to use the new
'NS R1rho 3-site' model synthetic data.
Added:
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site.py
- copied, changed from r21918,
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21923r1=21922r2=21923view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 18:08:58 2013
@@ -2440,6 +2440,16 @@
self.assertAlmostEqual(cdp.mol[0].res[0].spin[1].chi2, 0.0, 3)
+def test_ns_r1rho_3site(self):
+Compare the 'NS R1rho 3-site' dispersion model to synthetic data
from cpmg_fit.
+
+# Execute the script.
+self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_r1rho_3site.py')
+
+# Check the chi-squared value.
+self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2,
136.13141468674999, 3)
+
+
def test_ns_r1rho_3site_linear(self):
Compare the 'NS R1rho 3-site linear' dispersion model to synthetic
data from cpmg_fit.
Copied: trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site.py
(from r21918,
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site.py?p2=trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site.pyp1=trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.pyr1=21918r2=21923rev=21923view=diff
==
--- trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site.py Mon Dec
9 18:08:58 2013
@@ -12,7 +12,7 @@
# The path to the data files.
-DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'ns_r1rho_3site_linear'
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'ns_r1rho_3site'
# Create a data pipe.
@@ -96,7 +96,7 @@
relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
# Change the model.
-relax_disp.select_model('NS R1rho 3-site linear')
+relax_disp.select_model('NS R1rho 3-site')
# The R20 keys.
r20_600_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=600e6)
@@ -105,17 +105,17 @@
# Manually set the parameter values to the cpmg_fit solution with the
PEAK_SHIFT flag turned off.
spin = cdp.mol[0].res[0].spin[0]
spin.r2 = {
-r20_600_key: 8.000284037933310,
-r20_800_key: 9.000296050530716,
+r20_600_key: 8.168730946656503,
+r20_800_key: 9.129169123526795,
}
-spin.pA = 0.850029879276267
-spin.pB = 0.049922261890898
-spin.pC = 0.100047858832835
-spin.kex_AB = 500.991549690434681
-spin.kex_AC = 0.0
-spin.kex_BC = 2003.189830166320235
-spin.dw_AB = -2.991465198310455
-spin.dw_AC = 8.006033548997912
+spin.pA = 0.852219751988655
+spin.pB = 0.049881831108198
+spin.pC = 0.097898416903147
+spin.kex_AB = 597.092434638812506
+spin.kex_AC = 1000.000
+spin.kex_BC = 1922.815670008568304
+spin.dw_AB = -3.163019736662809
+spin.dw_AC = 7.985070582500403
spin.dw_BC = spin.dw_AC - spin.dw_AB
# Calculate.
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