r22219 - in /trunk: docs/latex/ graphics/screenshots/dispersion_analysis/
Author: bugman
Date: Thu Feb 20 10:39:34 2014
New Revision: 22219
URL: http://svn.gna.org/viewcvs/relax?rev=22219view=rev
Log:
Expanded the relaxation dispersion GUI tutorial in the manual.
This now includes the first steps for loading the peak intensity data.
Added:
trunk/graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup.eps.gz
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup.png
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_spin_name.eps.gz
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_spin_name.png
(with props)
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22219r1=22218r2=22219view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Thu Feb 20 10:39:34 2014
@@ -2715,7 +2715,7 @@
\item[Spin isotope:] This is needed to specify the spin isotope information
for each spin in the system, for example if the data is from $^{15}$N,
$^{13}$C, $^1$H, etc.
\item[$\Rone$ relaxation data:] This is used to load a text file containing
$\Rone$ relaxation data for each spin of interest.
The button launches the \uf{relax\_data.read} user function (see
section~\ref{uf: relax_data.read} on page~\pageref{uf: relax_data.read}).
-It is currently only used for properly handling off-resonance effects in
the $\Ronerho$-type dispersion data.
+It is currently only used for properly handling off-resonance effects in
the $\Ronerho$-type dispersion data but may be extended, in the future, to
handle off-resonance effects in the CPMG-type experiments.
\item[Chemical shift:] Again this is for properly handling off-resonance
effects in the $\Ronerho$-type dispersion data.
The button launches the \uf{chemical\_shift.read} user function (see
section~\ref{uf: chemical_shift.read} on page~\pageref{uf:
chemical_shift.read}).
\item[Interatomic interaction:] This button launches the
\uf{interatom.define} user function (see section~\ref{uf: interatom.define} on
page~\pageref{uf: interatom.define}).
@@ -2734,3 +2734,47 @@
In this case, all spins are $^{15}$N so simply leave the values to the
defaults and click on \guibutton{OK}.
The other buttons can be ignored.
+
+% Loading the data.
+%~~
+
+\subsection{Dispersion GUI mode -- loading the data}
+
+The standard way for handling experimental NMR data for starting a relaxation
dispersion analysis in the relax GUI is to load the peak intensity values
(either height or volume) from a peak list.
+For a list of all the currently supported peak list formats, see the
\uf{spectrum\ufsep{}read\ufus{}intensities} user function documentation in
section~\ref{uf: spectrum.read_intensities} on page~\pageref{uf:
spectrum.read_intensities}.
+
+Note that relax also accepts pre-fitted or pre-calculated $\Rtwoeff$ or
$\Ronerho$ values via the \uf{relax\ufus{}disp\ufsep{}r2eff\ufus{}read} and
\uf{relax\ufus{}disp\ufsep{}r2eff\ufus{}read\ufus{}spin} user functions (see
section~\ref{uf: relax_disp.r2eff_read} on page~\pageref{uf:
relax_disp.r2eff_read} and section~\ref{uf: relax_disp.r2eff_read_spin} on
page~\pageref{uf: relax_disp.r2eff_read_spin} respectively), however this is
not the standard way of using the GUI.
+As this is not tested, if you decide to work with pre-calculated relaxation
rates please report any bugs encountered as described in section~\ref{reporting
bugs} on page~\pageref{reporting bugs}.
+To access the user functions, click on \guimenuitemthree{User
functions}{relax\_disp}{r2eff\_read} or \guimenuitemthree{User
functions}{relax\_disp}{r2eff\_read\_spin}.
+
+In this tutorial, the Sparky\index{software!Sparky} formatted peak lists in
the
\directory{test\osus{}suite\ossep{}shared\osus{}data\ossep{}dispersion\ossep{}Hansen\ossep{}500\osus{}MHz}
and
\directory{test\osus{}suite\ossep{}shared\osus{}data\ossep{}dispersion\ossep{}Hansen\ossep{}800\osus{}MHz}
directories will be loaded.
+First click on the \guibutton{Add} button in the \gui{Spectra list} GUI
element.
+At this stage a warning message will appear as the spins have not been named,
hence they cannot be matched to the data in the peak lists:
+
+\begin{minipage}[h]{\linewidth}
+ \centerline{
+\includegraphics[
+ width=0.8\textwidth,
+ bb=14 14 1065 802
+]
+{graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup}
+ }
+\end{minipage}
+
+Simply click on \guibutton{Yes} to allow the spins to be named in the next
step.
+The \uf{spin\ufsep{}name} user function wizard page should now appear.
+
+\begin{minipage}[h]{\linewidth}
+ \centerline{
+\includegraphics[
+ width=0.8\textwidth,
+ bb=14 14 1065 802
+]
+
r22220 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: tlinnet Date: Thu Feb 20 18:15:43 2014 New Revision: 0 URL: http://svn.gna.org/viewcvs/relax?rev=0view=rev Log: Added the The relaxation time period to be used when returning cpmg frqs. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=0r1=22219r2=0view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Thu Feb 20 18:15:43 2014 @@ -2369,7 +2369,7 @@ return cpmg_frqs -def return_cpmg_frqs_single(exp_type=None, frq=None, offset=None, ref_flag=True): +def return_cpmg_frqs_single(exp_type=None, frq=None, offset=None, time=None, ref_flag=True): Return the list of nu_CPMG frequencies. @keyword exp_type: The experiment type. @@ -2378,6 +2378,8 @@ @type frq: float @keyword offset:The hard pulse offset, if desired. @type offset: None or float +@keyword time: The relaxation time period. +@type time: float @keyword ref_flag: A flag which if False will cause the reference spectrum frequency of None to be removed from the list. @type ref_flag: bool @return:The list of nu_CPMG frequencies in Hz. ___ 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
r22221 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: tlinnet Date: Thu Feb 20 18:16:39 2014 New Revision: 1 URL: http://svn.gna.org/viewcvs/relax?rev=1view=rev Log: Added test for skipping non-matching time points. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=1r1=0r2=1view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Thu Feb 20 18:16:39 2014 @@ -2412,6 +2412,10 @@ # Skip non-matching offsets. if offset != None and hasattr(cdp, 'spin_lock_offset') and cdp.spin_lock_offset[id] != offset: +continue + +# Skip non-matching time points. +if time != None and hasattr(cdp, 'relax_times') and cdp.relax_times[id] != time: continue # Skip non-matching points. ___ 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
r22224 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet Date: Thu Feb 20 18:17:11 2014 New Revision: 4 URL: http://svn.gna.org/viewcvs/relax?rev=4view=rev Log: Improved unit test for cathing both time and dispersion point when looping over experiment and time points. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=4r1=3r2=4view=diff == --- trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py (original) +++ trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Thu Feb 20 18:17:11 2014 @@ -54,15 +54,22 @@ cpmg_1 = [ncyc/time_T2_1 for ncyc in ncyc_1] cpmg_1.sort() -ncyc_2 = [28, 4, 32, 60, 2, 10, 16, 8, 20, 52, 18, 40, 6, 12, 24, 14] +ncyc_2 = [28, 4, 32, 60, 2, 10, 16, 8, 20, 52, 18, 40, 6, 12, 24, 14, 22] sfrq_2 = 599.8908587*1E6 time_T2_2 = 0.06 cpmg_2 = [ncyc/time_T2_2 for ncyc in ncyc_2] cpmg_2.sort() # Test the loop function. +# First initialize index for the two lists. +i = -1 +j = -1 for exp_type, frq, offset, point, time, ei, mi, oi, di, ti in loop_exp_frq_offset_point_time(return_indices=True): if frq == sfrq_1: +i += 1 self.assertEqual(time, time_T2_1) +self.assertAlmostEqual(point, cpmg_1[i],3) if frq == sfrq_2: +j += 1 self.assertEqual(time, time_T2_2) +self.assertAlmostEqual(point, cpmg_2[j],3) ___ 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
r22222 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: tlinnet Date: Thu Feb 20 18:16:51 2014 New Revision: 2 URL: http://svn.gna.org/viewcvs/relax?rev=2view=rev Log: Switched the looping over time points and dispersion points. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=2r1=1r2=2view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Thu Feb 20 18:16:51 2014 @@ -869,10 +869,10 @@ for frq, mi in loop_frq(return_indices=True): # Then loop over the offset data. for offset, oi in loop_offset(exp_type=exp_type, frq=frq, return_indices=True): -# Then the dispersion points. -for point, di in loop_point(exp_type=exp_type, frq=frq, offset=offset, return_indices=True): -# Finally the relaxation times. -for time, ti in loop_time(return_indices=True): +# Then the relaxation times. +for time, ti in loop_time(return_indices=True): +# Finally the dispersion points. +for point, di in loop_point(exp_type=exp_type, frq=frq, offset=offset, time=time, return_indices=True): # Yield the data. if return_indices: yield exp_type, frq, offset, point, time, ei, mi, oi, di, ti ___ 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
