Author: bugman
Date: Fri Feb 21 16:08:36 2014
New Revision: 22238
URL: http://svn.gna.org/viewcvs/relax?rev=22238&view=rev
Log:
Continued expanding the tutorial for performing a relaxation dispersion
analysis in the GUI.
This is for the dispersion chapter of the manual.
Added:
trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection.eps.gz
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection.png
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection_fin.eps.gz
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection_fin.png
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_spectrum_ids.eps.gz
(with props)
trunk/graphics/screenshots/dispersion_analysis/spectrum_spectrum_ids.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=22238&r1=22237&r2=22238&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Fri Feb 21 16:08:36 2014
@@ -2616,24 +2616,24 @@
After starting relax in the GUI mode, the dispersion analysis should be
initialised by launching the analysis selection wizard (see Figure~\ref{fig:
screenshot: analysis wizard} on page \pageref{fig: screenshot: analysis
wizard}).
The relaxation dispersion analysis should be selected and the name changed
if multiple dispersion analyses are to be performed within one relax session.
-In this case the name \gui{Dispersion - Hansen (non-clustered)} will be used.
+In this case the name \gui{Dispersion - Hansen (non-clustered)} will be used:
\begin{minipage}[h]{\linewidth}
\centerline{
\includegraphics[
- width=0.8\textwidth,
+ width=0.9\textwidth,
bb=14 14 1065 802
]
{graphics/screenshots/dispersion_analysis/analysis_wizard1}
}
\end{minipage}
-Click on the \guibutton{Next} button to move to the second wizard page.
+Click on the \guibutton{Next} button to move to the second wizard page:
\begin{minipage}[h]{\linewidth}
\centerline{
\includegraphics[
- width=0.8\textwidth,
+ width=0.9\textwidth,
bb=14 14 1065 802
]
{graphics/screenshots/dispersion_analysis/analysis_wizard2}
@@ -2654,7 +2654,7 @@
\begin{minipage}[h]{\linewidth}
\centerline{
\includegraphics[
- width=0.8\textwidth,
+ width=0.9\textwidth,
bb=14 14 1065 802
]
{graphics/screenshots/dispersion_analysis/blank}
@@ -2728,7 +2728,13 @@
For SQ CPMG-type dispersion data, only the spin isotope information is
required.
\begin{minipage}[h]{\linewidth}
-\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1065
802]{graphics/screenshots/dispersion_analysis/spin_isotope}}
+ \centerline{
+ \includegraphics[
+ width=0.9\textwidth,
+ bb=14 14 1065 802
+ ]
+ {graphics/screenshots/dispersion_analysis/spin_isotope}
+ }
\end{minipage}
In this case, all spins are $^{15}$N so simply leave the values to the
defaults and click on \guibutton{OK}.
@@ -2754,7 +2760,7 @@
\begin{minipage}[h]{\linewidth}
\centerline{
\includegraphics[
- width=0.8\textwidth,
+ width=0.9\textwidth,
bb=14 14 1065 802
]
{graphics/screenshots/dispersion_analysis/spectrum_incomplete_setup}
@@ -2762,12 +2768,12 @@
\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.
+The \uf{spin\ufsep{}name} user function wizard page should now appear:
\begin{minipage}[h]{\linewidth}
\centerline{
\includegraphics[
- width=0.8\textwidth,
+ width=0.9\textwidth,
bb=14 14 1065 802
]
{graphics/screenshots/dispersion_analysis/spectrum_spin_name}
@@ -2776,5 +2782,129 @@
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.
-
+
+To help to understanding the next steps of the peak intensity loading
wizard, please take note of the following table which summarises the peak
list metadata for this analysis:
+
+\begin{center}
+\begin{footnotesize}
+\begin{tabular}{llllll}
+\toprule
+
+File name & Spectrum ID & Spectrometer & $\nucpmg$ & Replicate \\
+ & & frq. (MHz) & (Hz) & IDs \\
+
+\midrule
+
+\file{500\osus{}MHz\ossep{}reference.in\osus{}sparky} & 500\_ref &
500.0 & None & \\
+\file{500\osus{}MHz\ossep{}133.33.in\osus{}sparky} & 500\_133.33 &
500.0 & 66.6666 & 500\_133.33b \\
+\file{500\osus{}MHz\ossep{}133.33.in.bis\osus{}sparky} & 500\_133.33b &
500.0 & 133.3333 & 500\_133.33 \\
+\file{500\osus{}MHz\ossep{}200.in\osus{}sparky} & 500\_200.00 &
500.0 & 133.3333 & \\
+\file{500\osus{}MHz\ossep{}266.67.in\osus{}sparky} & 500\_266.67 &
500.0 & 200.0000 & \\
+\file{500\osus{}MHz\ossep{}333.33.in\osus{}sparky} & 500\_333.33 &
500.0 & 266.6666 & \\
+\file{500\osus{}MHz\ossep{}400.in\osus{}sparky} & 500\_400.00 &
500.0 & 333.3333 & \\
+\file{500\osus{}MHz\ossep{}466.67.in\osus{}sparky} & 500\_466.67 &
500.0 & 400.0000 & \\
+\file{500\osus{}MHz\ossep{}533.33.in\osus{}sparky} & 500\_533.33 &
500.0 & 466.6666 & 500\_533.33b \\
+\file{500\osus{}MHz\ossep{}533.33.in.bis\osus{}sparky} & 500\_533.33b &
500.0 & 533.3333 & 500\_533.33 \\
+\file{500\osus{}MHz\ossep{}600.in\osus{}sparky} & 500\_600.00 &
500.0 & 533.3333 & \\
+\file{500\osus{}MHz\ossep{}66.667.in\osus{}sparky} & 500\_66.667 &
500.0 & 600.0000 & \\
+\file{500\osus{}MHz\ossep{}666.67.in\osus{}sparky} & 500\_666.67 &
500.0 & 666.6666 & \\
+\file{500\osus{}MHz\ossep{}733.33.in\osus{}sparky} & 500\_733.33 &
500.0 & 733.3333 & \\
+\file{500\osus{}MHz\ossep{}800.in\osus{}sparky} & 500\_800.00 &
500.0 & 800.0000 & \\
+\file{500\osus{}MHz\ossep{}866.67.in\osus{}sparky} & 500\_866.67 &
500.0 & 866.6666 & \\
+\file{500\osus{}MHz\ossep{}933.33.in\osus{}sparky} & 500\_933.33 &
500.0 & 933.3333 & 500\_933.33b \\
+\file{500\osus{}MHz\ossep{}933.33.in.bis\osus{}sparky} & 500\_933.33b &
500.0 & 933.3333 & 500\_933.33 \\
+\file{500\osus{}MHz\ossep{}1000.in\osus{}sparky} & 500\_1000.0 &
500.0 & 1000.0000 & \\
+ \\
+\file{800\osus{}MHz\ossep{}reference.in\osus{}sparky} & 800\_ref &
800.0 & None & \\
+\file{800\osus{}MHz\ossep{}133.33.in\osus{}sparky} & 800\_133.33 &
800.0 & 66.6666 & 800\_133.33b \\
+\file{800\osus{}MHz\ossep{}133.33.in.bis\osus{}sparky} & 800\_133.33b &
800.0 & 133.3333 & 800\_133.33 \\
+\file{800\osus{}MHz\ossep{}200.in\osus{}sparky} & 800\_200.00 &
800.0 & 133.3333 & \\
+\file{800\osus{}MHz\ossep{}266.67.in\osus{}sparky} & 800\_266.67 &
800.0 & 200.0000 & \\
+\file{800\osus{}MHz\ossep{}333.33.in\osus{}sparky} & 800\_333.33 &
800.0 & 266.6666 & \\
+\file{800\osus{}MHz\ossep{}400.in\osus{}sparky} & 800\_400.00 &
800.0 & 333.3333 & \\
+\file{800\osus{}MHz\ossep{}466.67.in\osus{}sparky} & 800\_466.67 &
800.0 & 400.0000 & \\
+\file{800\osus{}MHz\ossep{}533.33.in\osus{}sparky} & 800\_533.33 &
800.0 & 466.6666 & \\
+\file{800\osus{}MHz\ossep{}533.33.in.bis\osus{}sparky} & 800\_533.33b &
800.0 & 533.3333 & 800\_533.33b \\
+\file{800\osus{}MHz\ossep{}600.in\osus{}sparky} & 800\_600.00 &
800.0 & 533.3333 & 800\_533.33 \\
+\file{800\osus{}MHz\ossep{}66.667.in\osus{}sparky} & 800\_66.667 &
800.0 & 600.0000 & \\
+\file{800\osus{}MHz\ossep{}666.67.in\osus{}sparky} & 800\_666.67 &
800.0 & 666.6666 & \\
+\file{800\osus{}MHz\ossep{}733.33.in\osus{}sparky} & 800\_733.33 &
800.0 & 733.3333 & \\
+\file{800\osus{}MHz\ossep{}800.in\osus{}sparky} & 800\_800.00 &
800.0 & 800.0000 & \\
+\file{800\osus{}MHz\ossep{}866.67.in\osus{}sparky} & 800\_866.67 &
800.0 & 866.6666 & \\
+\file{800\osus{}MHz\ossep{}933.33.in\osus{}sparky} & 800\_933.33 &
800.0 & 933.3333 & 800\_933.33b \\
+\file{800\osus{}MHz\ossep{}933.33.in.bis\osus{}sparky} & 800\_933.33b &
800.0 & 933.3333 & 800\_933.33 \\
+\file{800\osus{}MHz\ossep{}1000.in\osus{}sparky} & 800\_1000.0 &
800.0 & 1000.0000 & \\
+
+\bottomrule
+\end{tabular}
+\end{footnotesize}
+\end{center}
+
+For all of these files, the experiment type is SQ CPMG and the relaxation
delay time is 30~ms.
+All files are located in the
\directory{test\osus{}suite\ossep{}shared\osus{}data\ossep{}dispersion\ossep{}Hansen}
directory.
+
+To simplify the loading of the data, all of the 500 MHz data will be read
simultaneously (followed by all of the 800 MHz data).
+Firstly, to select all of the 500~MHz files, click on the button at the end
of the \guistring{file name(s)} GUI element.
+This will launch the multiple file selection window:
+
+\begin{minipage}[h]{\linewidth}
+ \centerline{
+ \includegraphics[
+ width=0.9\textwidth,
+ bb=14 14 1415 1065
+ ]
+ {graphics/screenshots/dispersion_analysis/spectrum_file_selection}
+ }
+\end{minipage}
+
+Add the first file by typing the file name or clicking on the file selection
button to the right of the file input field and choosing the file.
+A preview button is included to allow the file to be checked.
+Then click on the \guibutton{Add} button to insert a new file selection
item, add the next file, and continue until complete.
+You should now see:
+
+\begin{minipage}[h]{\linewidth}
+ \centerline{
+ \includegraphics[
+ width=0.9\textwidth,
+ bb=14 14 1415 1065
+ ]
+ {graphics/screenshots/dispersion_analysis/spectrum_file_selection_fin}
+ }
+\end{minipage}
+
+Click on \guibutton{OK} to return to the
\uf{spectrum\ufsep{}read\ufus{}intensities} user function wizard page.
+Next, the spectrum IDs should be set.
+For this, click on the button to the far right of the spectrum ID string
element.
+Click on \guibutton{Add} and fill in the spectrum IDs corresponding to the
files selected.
+As 19 files exist for the 500 MHz data, 19 spectrum IDs should be added.
+You will now see:
+
+\begin{minipage}[h]{\linewidth}
+ \centerline{
+ \includegraphics[
+ width=0.9\textwidth,
+ bb=14 14 1415 1065
+ ]
+ {graphics/screenshots/dispersion_analysis/spectrum_spectrum_ids}
+ }
+\end{minipage}
+
+Click on \guibutton{OK} to return to the
\uf{spectrum\ufsep{}read\ufus{}intensities} user function wizard page.
+
+There is one shortcut to these previous steps.
+The file names and spectrum IDs can be manually typed into the input
elements of the \uf{spectrum\ufsep{}read\ufus{}intensities} user function
wizard page.
+For the file names, assuming relax is installed in the directory
\directory{data\ossep{}relax\ossep{}relax-trunk} and a Unix-like system is
being used, the following text can be added:
+\begin{lstlisting}[numbers=none]
+['/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/reference.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/200.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/266.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/333.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/400.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/466.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in.bis_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/600.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/66.667.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/666.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/733.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/800.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/866.67.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in.bis_sparky',
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Hansen/500_MHz/1000.in_sparky']
+\end{lstlisting}
+
+The spectrum IDs can be added by copying and pasting the following text:
+\begin{lstlisting}[numbers=none]
+['500_reference', '500_133.33', '500_133.33b', '500_200', '500_266.67',
'500_333.33', '500_400', '500_466.67', '500_533.33', '500_533.33b',
'500_600', '500_66.667', '500_666.67', '500_733.33', '500_800', '500_866.67',
'500_933.33', '500_933.33b', '500_1000']
+\end{lstlisting}
+
+Note that the files can also be loaded one by one.
+
+For this SQ CPMG data, none of the other settings in the
\uf{spectrum\ufsep{}read\ufus{}intensities} user function wizard page need to
be changed.
+But clicking on the \guibutton{Apply} button, the 500 MHz data will be
loaded but the wizard will stay on the same page.
+This will allow the 800 MHz data to also be loaded.
Added:
trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection.eps.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection.eps.gz?rev=22238&view=auto
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trunk/graphics/screenshots/dispersion_analysis/spectrum_file_selection.png
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r22238 - in /trunk: docs/latex/ graphics/screenshots/dispersion_analysis/
