Author: bugman
Date: Thu Feb 20 10:39:34 2014
New Revision: 22219
URL: http://svn.gna.org/viewcvs/relax?rev=22219&view=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=22219&r1=22218&r2=22219&view=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
+ ]
+ {graphics/screenshots/dispersion_analysis/spectrum_spin_name}
+ }
+\end{minipage}
+
+As all data is from $^{15}$N spins and these spins have been named as `N' in
the Sparky peak lists, set the new spin name to \guistring{N} and click on
\guibutton{Next}.
+The \uf{spectrum\ufsep{}read\ufus{}intensities} user function wizard page
should appear.
+To simplify the loading, all of the 500 MHz data will be loaded in one go.
+
Added:
trunk/graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup.eps.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup.eps.gz?rev=22219&view=auto
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Added:
trunk/graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup.png
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup.png?rev=22219&view=auto
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Added:
trunk/graphics/screenshots/dispersion_analysis/spectrum_spin_name.eps.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/dispersion_analysis/spectrum_spin_name.eps.gz?rev=22219&view=auto
==============================================================================
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Added: trunk/graphics/screenshots/dispersion_analysis/spectrum_spin_name.png
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/dispersion_analysis/spectrum_spin_name.png?rev=22219&view=auto
==============================================================================
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svn:mime-type = image/png
r22219 - in /trunk: docs/latex/ graphics/screenshots/dispersion_analysis/
