## Please note that all actions from all_tutorials_preamble.txt will be added here!

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c:showQ True

p:Welcome to this first demo introducing you to *Olex2*. To get the most out of it, please read this text carefully and when you are done press the _Next_ button.

p:You can exit the tutorial window to move the molecule in the graphics window if you like.<br>If you would like to use the Graphical User Interface (GUI) properly, press _cancel_ and leave the tutorial.

p:Structures are loaded from the **Start** tool. The tool will be highlighted when you press _Next_.

h:h2-Start
c:html.ItemState home-start 1
c:reset

p:You can choose a sample structure by clicking one of the links next to the title **Sample Structure**. In this tutorial, we will be solving and refining one of the sample structures that come with OLEX2 - "SUCROSE". Please press <c>Next</c> to load it (this may take some time!).
c:refresh
c:freeze(true)
c:reap DataDir()/samples/sucrose/sucrose.res
c:spy.revert_to_original()
c:mpln -n
c:freeze(false)
c:refresh

p:By clicking on the **Work** tab, we get access to the main tools in OLEX2:
h:tab-work;3
c:spy.demo.switch_tab_for_tutorials(work)

p:Structure **Solution**, **Refinement** and **Reports**
h:btn-solve;3
h:btn-refine;3
h:btn-report;3

p:To solve your crystal structure with OLEX2 you need to provide a reflection file (**name.hkl**) and an input file (name.ins) containing the crystallographic unit cell you determined during the diffraction experiment.

p:We can solve the structure of our example sucrose by typing <c>solve</c> into the graphics window or by clicking the **Solve** button. We will do this now.
h:btn-solve;1
c:solve
c:waitfor process
c:refresh

p:We can tidy this solution by typing _clean_ or by pressing the **Clean** button.
h:toolbar-tidy
c:clean
c:compaq -a
c:refresh

p:Let's press the **Refine** button or type <c>refine</c> and refine what we've got so far.
h:btn-refine;1
c:refine

p:For every instruction that you can use in the graphics window, a short help description tells you the function and possibly switches. If you type <c>help clean</c>...
c:help clean
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p:...the macro Clean is described in the graphics window. Let's clean once again.
c:clean

p:With the **Uiso Slider** in the **Toolbox Work** we can select all those atoms that look 'too small'
c:html.ItemState work-main-toolbar 1
c:html.ItemState h3-peak-and-uiso-sliders 1
c:html.setBG(UISO_SELECT_SLIDER,#ff0000)
c:html.setvalue(UISO_SELECT_SLIDER,-7)
c:html.setvalue(UisoSelectVal,<0.035)
c:sel atoms where xatom.uiso < 0.035&&xatom.type!='Q'
c:refresh

p:... and make them into Oxygen by pressing the **O** button.
h:btn-elementO
c:name sel O
c:refresh

p:Refine this again...
c:refine

p:Clean...
c:clean

p:Now it's time to make everything **anisotropic**. Type <c>anis</c> or click on the **ANIS** button.
h:toolbar-ANIS
c:anis
c:refine

p:... clean it ...
c:clean

p:Let's add some hydrogen atoms to this. Type <c>hadd</c> or click on the **ADD H** button:
h:small-Add_H
c:hadd
c:refine
c:refresh

p:You can toggle the display of electron density peaks (Q-peaks) by repeatedly pressing the **Q** button or by <c>CTRL+Q</c>
h:toolbar-q
c:showQ False
c:refresh
##

p:Of course, we can change the settings of the solution program.

p:We do this, by clicking the **Solution Settings** Button.
h:cbtn-solve
c:html.ItemState solve-settings 1


p:Here we can choose solution programs and settings ...
h:SET_snum_solution_PROGRAM_bg
h:SET_snum_solution_METHOD_bg

p:... set the **Formula** and can determine the **space group**.
h:SET_SNUM_REFINEMENT_FORMULA_bg
h:SET_SNUM_REFINEMENT_SPACE_GROUP_bg

p:When you click on **Suggest SG** link, or type <c>sg</c>, watch what happens in the graphics window!
c:sg
c:refresh

p:In order to see all the console output in the graphics window, you can type <c>lines -1</c>.
c:lines -1
c:refresh

p:To show only 10 lines, type <c>lines 10</c>
c:lines 10
c:refresh
c:html.ItemState solve-settings 2

p:If you type <c>text</c> or press the little text icon, you will get a 'transcript' of the console in your text editor
h:toolbar-text
c:text
c:refresh

p:To clear the console output, type <c>clear</c>
c:clear
c:refresh
c:html.ItemState solve-settings 2

p:We hope you enjoyed this first introduction to <font color="rgb(255,100,50)">OLEX2</font color="rgb(255,100,50)"> - please let us know if we missed out any essential steps in this manual by visiting www.olex2.org and getting engaged in the OLEX2 development.


c:spy.demo.switch_tab_for_tutorials(home)
p:End of tutorial, press next to repeat the tutorial or cancel to exit. <br><font size='1'>Written by Stefanie Freitag-Pohl.</font>