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Merge pull request #1 from KlasJoenssson/UpdateCheatSheet
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Updates of the cheat sheets.
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@egonw
egonw committed Mar 12, 2012
2 parents a1c1a38 + d8cfe67 commit a2af335
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16 changes: 8 additions & 8 deletions plugins/net.bioclipse.nmrshiftdb/cheatsheets/SubmitCheatSheet.xml
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<intro>
<description>
This cheat sheet gives you a tutorial on how to submit data to NMRShiftDB. It will guide you through the process of submitting a structure and a spectrum to NMRShiftDB.
Note that the order of the steps is partly open to you, also some elements may be obmitted either because you get the data from somewhere else or because you do not need them.
Note that the order of the steps is partly open to you, also some elements may be omitted either because you get the data from somewhere else or because you do not need them.
We will try to make clear where this is the case.
</description>
</intro>
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<item title="Step 1: Creating the structure file">
<description>
The first thing you need is a file containing the structure you want to submit. If you do no yet have this from another source, you can use the JChemPaint plugin to draw your structure and save it (we
recommand the CML file format). To create a new structure file, use "File"->"New ..."->"Chemistry"->"Molecule" (or use the "Click to perform" below). You can then open the new file by double clicking it and draw the molecule. If you need
help on drawing, use the "Help"->"Help Contents"->"JChemPaint". If your spectra include a 1H spectrum, and you want to assign different shifts to protons at the same heavy atom, you need to have explicit protons there. You can make all protons explicit via "JChempaint"->"Edit"->"Hydrogens ..."->"Make all hydrogens explicit" (in your final submission only protons around chiral centers will be visible, though). Once you have finished the structure save it.
recommand the CML file format). To create a new structure file, use <b>File > New... > Chemistry > Molecule</b> (or use the "Click to perform" below). You can then open the new file by double clicking it and draw the molecule. If you need
help on drawing, use the <b>Help > Help Contents > JChemPaint</b>. If your spectra include a 1H spectrum, and you want to assign different shifts to protons at the same heavy atom, you need to have explicit protons there. You can make all protons explicit via <b>JChempaint > Edit > Hydrogens... > Make all hydrogens explicit</b> (in your final submission only protons around chiral centers will be visible, though). Once you have finished the structure save it.
</description>
<action pluginId="net.bioclipse.nmrshiftdb" class="net.bioclipse.nmrshiftdb.actions.CheatSheetAction" param1="newstruc">
</action>
</item>
<item title="Step 2: Creating the spectrum (or spectra)">
<description>
The second thing you need is a file containing the spectrum you want to submit. This can be in JCAMP-DX or CML format. If you do no yet have this from another source, you can use the Spectrum plugin to type your spectrum and save it (we
recommand the CML file format). To create a new spectrum file, use "File"->"New ..."->"Spectrum"->"New Spectrum" (or use the "Click to perform" below). After presssing "Finish", you can open the new file by double clicking it and add the desired peaks.
If you need help, use "Help"->"Help Contents"->"The Spectrum Plugin". Once you have finished the spectrum save it. If you want several spectra (e. g. different nuclei) for the structure, you need to repeat this step.
recommand the CML file format). To create a new spectrum file, use <b>File > New... > Spectrum > New Spectrum</b> (or use the "Click to perform" below). After pressing "Finish", you can open the new file by double clicking it and add the desired peaks.
If you need help, use <b>Help > Help Contents > The Spectrum Plugin</b>. Once you have finished the spectrum save it. If you want several spectra (e. g. different nuclei) for the structure, you need to repeat this step.
</description>
<action pluginId="net.bioclipse.nmrshiftdb" class="net.bioclipse.nmrshiftdb.actions.CheatSheetAction" param1="newspec"/>
</item>
<item title="Step 3: Creating a literature entry (optional)">
<description>
If you do not want to have a literature entry in your submission, you can skip this step. If you want a literature entry, you need to have it in a BibTex file. You can take any BibTex tool you like or
create one via "File"->"New ..."->"BibTex"->"New bibtex file". We recommand to use the template. You can then open the new file by double clicking it and copy/paste the template for your literature type and fill it in. Once you have finished save it.
create one via <b>File > New... > Other > New bibtex file</b>. We recommend to use the template. You can then open the new file by double clicking it and copy/paste the template for your literature type and fill it in. Once you have finished save it.
</description>
</item>
<item title="Step 4: Bringing it all together">
<description>
You now have got the components you need and just want to combine them. For doing this, create a new "Spectrum and Molecule" file via "File"->"New ..."->"SpecMol"->"New Assigend Spectrum" (or use the "Click to perform" below). You first need to choose a name for your file (it will get the extension cml, so you need to choose a different name in case you already use cml files for
You now have got the components you need and just want to combine them. For doing this, create a new "Spectrum and Molecule" file via <b>File > New... > Spectrum related > New Assigned Spectrum</b> (or use the "Click to perform" below). You first need to choose a name for your file (it will get the extension cml, so you need to choose a different name in case you already use cml files for
structure or spectrum), then to choose the structure to include (normally the one you entered in step1) and finally the spectra (normally the spectra from step 2). Clicking "Finish" will give you a file ending with cml which you can open by double click and which shows you the structure
and one of your spectra (you can change between them in the outline view). Almost the only thing left are the assignments.
</description>
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<item title="Step 6: The actual submit">
<description>
So, you have got all your data. To submit it, right click on the assigned spectrum file created in Step 4 and choose the "Submit to NMRShiftDB" item. A window pops up which requieres you to fill in certain metadata, if not yet done with the spectrum. After that, you are asked for the NMRShiftDB username and password. If you press "Finish", your data go
off to the server. Congratulations and thanks! If you need more detailed info on the actual submit, see the help at "Help"->"Help contents"->"NMRShiftDB plugin"->"About NMRShiftDB plugin"->"Submit to NMRShiftDB".
off to the server. Congratulations and thanks! If you need more detailed info on the actual submit, see the help at <b>Help > Help contents > NMRShiftDB plugin > About NMRShiftDB plugin > Submit to NMRShiftDB</b>.
</description>
</item>
</cheatsheet>
32 changes: 17 additions & 15 deletions plugins/net.bioclipse.spectrum/cheatsheets/GeneralSpectrumCheatSheet.xml
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@@ -1,22 +1,24 @@
<?xml version="1.0" encoding="UTF-8"?>
<cheatsheet title="General Spectrum Cheatsheet">
<cheatsheet title="General Spectrum Cheat Sheet">
<intro>
<description>
This cheat sheet tells you about things you can do with spectra in Bioclipse.
Note that each step in this cheat sheet is in independent task, so there is no order and steps do not depend on each other.
Note that each step in this cheat sheet is an independent task, so there is no order and steps do not depend on each other.
</description>
</intro>
<item title="Step 0: Prerequisites">
<description>
You need the Speclipse feature installed for this (which you have if you read this and installed via the update site).
You need the Speclipse feature installed for this (which you have if you read this and installed via the update site). If you don't have any spectrum files,
there's a good idea to create a new Speclipse Sample Data Project before starting with this cheat sheet. This is done by choosing <b>File > New… > Data >
Speclipse Sample Data Project</b>.
</description>
</item>
<item
href="/net.bioclipse.spectrum/doc/spectrumEditor.html"
title="Option 1: Analyze spectra">
title="Step 1: Analyze spectra">
<description>
The spectrum editor shows spectrum files in any of the allowed formats (see help via ? on top of this section for details). By default, spectrum files
will open in it. If they do not, right click the file and choose Open with -> Spectrum Editor. The editor gives you an insight
will open in it. If they do not, right click the file and choose <b> Open with > Spectrum Editor </b>. The editor gives you an insight
into the content of the file. See the help for explanations. If you want to compare several spectra, you can use the
Compare Spectra view. Open it with the link below and choose as many peak spectra files as you like in the navigator (hold Ctrl). They
will be shown in the same scale (it only makes sense to compare spectra of the same type, e. g. 1H-NMR). Files not
Expand All @@ -26,14 +28,14 @@
</item>
<item
href="/net.bioclipse.spectrum/doc/spectrumEditor.html"
title="Option 2: Perform a peak picking">
title="Step 2: Perform a peak picking">
<description>
When a file is open in the spectrum editor, you can perform a peak picking via the "Pick peaks" icon in the toolbar.
</description>
</item>
<item
href="/net.bioclipse.spectrum/doc/new.html"
title="Option 3: Creating a new (peak) spectrum">
title="Step 3: Creating a new (peak) spectrum">
<description>
You can create a new spectrum in Speclipe. In practice, this is restricted to peak spectra since you need to enter
the data yourself. See help via ? on top of this section for details.
Expand All @@ -42,37 +44,37 @@
</item>
<item
href="/net.bioclipse.spectrum/doc/formats.html"
title="Option 4: Convert file formats">
title="Step 4: Convert file formats">
<description>
If you have a spectrum file open, you can save it in another format using the Save As... option.
</description>
<action pluginId="net.bioclipse.spectrum" class="net.bioclipse.spectrum.action.CheatSheetAction" param1="saveas"/>
</item>
<item
href="/net.bioclipse.nmrshiftdb/html/search.html#searchbyspectrum"
title="Option 5: Find out which structure might be behind an NMR spectrum">
title="Step 5: Find out which structure might be behind an NMR spectrum">
<description>
If you have a peak-picked NMR spectrum, you can try to find out what structure was recorded via searching in
NMRShiftDB. Right click on your spectrum in the navigator and choose "Spectrum Search in NMRShiftDB...". For
NMRShiftDB. Right click on your spectrum in the navigator and choose <b>Spectrum Search in NMRShiftDB..."</b>. For
details, click ? on top of this section.
</description>
</item>
<item
href="/net.bioclipse.nmrshiftdb/html/predict.html"
title="Option 6: Get the NMR spectrum for a structure">
title="Step 6: Get the NMR spectrum for a structure">
<description>
If you want to know what the NMR spectrum of a structure would look like, there are two options: Firstly you can
search NMRShiftDB for it. Right-click your structure in the navigator and choose "Download NMR spectra for this molecule...". This
search NMRShiftDB for it. Right-click your structure in the navigator and choose <b>Download NMR spectra for this molecule...</b>. This
will give you a measured, accurate spectrum given it is in NMRShiftDB. If not, you have the second option of predicting the spectrum
via "Spectrum Prediction"->"NMR from NMRShiftDB". This will give you a result in any case. In most cases this will closely match the
via <b>Spectrum Prediction > NMR from NMRShiftDB</b>. This will give you a result in any case. In most cases this will closely match the
real spectrum, but in rare cases (e. g. exotic elements in your structure) the results can be inaccurate.
</description>
</item>
<item
href="/net.bioclipse.nmrshiftdb/html/submit"
title="Option 7: Assign an (NMR-)spectrum and perhapssubmit it to NMRShiftDB">
title="Step 7: Assign an (NMR-)spectrum and perhapssubmit it to NMRShiftDB">
<description>
There is a separate cheat sheet for this. Click the arrow in the top bar of this cheat sheet and choose "NMRShiftDB Submit Cheat Sheet" or
There is a separate cheat sheet for this. Click the arrow in the top bar of this cheat sheet and choose <b>NMRShiftDB Submit Cheat Sheet</b> or
read the help available via the ?.
</description>
</item>
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