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== SPARKY GUI ==
The keyboard shortcuts are listed in the manual [http://www.cgl.ucsf.edu/home/sparky/manual/indx.html]
First make window bigger.<br>
'''zo''' for zoom out. '''zi''' Zoom in.
'''ct''' for setting countour level. <br>
Set level 6 for positive and negative.<br>
Add 1 to the +e0x level. Ex: xxxe+03 -> xxxe+04 ind positive and negative.<br>
Ok
'''rp''' for read peaks. Find your peak file.<br>
../peak_lists/peaks.list
Click Create peaks, Close.
Then go through our peaks, to center them.<br>
'''lt''' (LT) to show a list of peaks for a spectrum.<br>
Double click on peak "A3N" in the list. Zoom in "zi".
Now you want to align you peaks, since they can be off-shifted.<br>
First note down the current value of PPM in w1 and w2. <br>
A3N-HN 121.828 8.513
Push '''F1''' for select mode, drag it with the mouse or "pc" for auto "peak center". <br>
Then click "Update" in the peak list, and note down the new values. <br>
A3N-HN 121.681 8.514
We need to shift the nitrogen peaks
(121.681 - 121.828)=-0.147 ppm,
and proton peaks
(8.514 - 8.513)=0.001 ppm.
Exit SPARKY
== Shift all peaks ==
Go to the peak_list folder.
<source lang="bash">
cd ../peak_lists/
</source>
Correct Nitrogen
<source lang="bash">
sparky_add.sh peaks.list '$2' -0.147 peaks_corr_N15.list
</source>
Correct Proton
<source lang="bash">
sparky_add.sh peaks_corr_N15.list '$3' 0.001 peaks_corr_N15_1H.list
</source>
Now go into Sparky again, and read peak list.
<source lang="bash">
cd ..
cd spectrometer_data_processed
sparky 0.fid/test.ucsf
</source>
'''rp''' Choose '''../peak_lists/peaks_corr_N15_1H.list''' <br>
Create peaks, close.<br>
'''zo''' zoom out. '''ct''' set contour. <br>
'''lt''' and go through peaks, and auto center with '''pc'''.<br>
Problematic peaks:<br>
H30N-HN, not possible to auto center in the middle. Next to L47 and E4.
A57N-HN / D68N-HN In original peak list: A57N-HN 121.526 7.944 / D68N-HN 121.511 7.922, both centered to: 121.409 7.933.
Save file to: '''../peak_lists/peaks_corr_peak_center.list''' and then alter values manual.
<source lang="bash">
cp ../peak_lists/peaks_corr_peak_center.list ../peak_lists/peaks_corr_final.list
gedit ../peak_lists/peaks_corr_final.list &
</source>
= See also =
[[Category:Tutorials]]
