#set:bg_colour=gui.html.bg_colour
#set:font_colour=gui.html.font_colour

set:font_colour_code=#aaaaff
set:font_colour_bold=gui.html.highlight_colour

c:itemstate index* 0
c:itemstate index-home 1
c:itemstate tab* 2
c:lines 10
c:showq false

p:This tutorial will show you how to use grow on a molecule in order to demonstrate how molecules interact with each other within the structure

p:First we need to load an extended structure model so for this we will use <b>ZZULI2</b> from the <b>sample structures</b>
c:freeze(true)
c:reap 'DataDir()/samples/ZZULI2/ZZULI2.res'
c:spy.revert_to_original()
c:mpln -n
c:freeze(false)
c:refresh

p:The next thing to do in order to help keep all of the molecule in view is to set the command window to automatic zoom so that it keeps the molecule in view at all times.

p:To do this in the command line enter <c>echo extrazoom()</c> to check what the default value is set to this should usually be <b>1.25</b>
c:echo extrazoom()

p:Once you've checked the value you can change it to any value you want here we are going to change it to 1 so enter in <c>echo extrazoom(1)</c>
c:echo extrazoom(1)

p:This should now make the screen automatically zoom in and out to fit the molecule to the right proportions

p:In order to make the molecule grow we need to click on the tab marked <b>View</b>.
h:tab-view
c:spy.switch_tab_for_tutorials(view)

p:Then click on the tab marked <b>Symmetry Generation</b>
h:h2-symmetry-generation
c:itemstate view-symmetry-generation 1

p:Click on the tab marked <b>Growing</b> in order to access some of the different grow modes.
h:h3-h3-growing
c:itemstate h3-growing 1

p:In the expanded tab it now means you can select 3 different modes of growing.

p:<b>Short</b> which allows you to grow the molecule by one extra molecule each time in order to show short intermolecular interactions between molecules.
c:html.setbg(GROW_SHORT,red)
c:html.setstate(GROW_SHORT,true)

p:In order to then cause the molecule to grow you have to select the button <b>Grow Mode</b>.
h:button-grow_mode
c:run(mode grow GetData(GROW_SHORT) GetData(GROW_SELECTION) GetData(GROW_VDW))

p:You can now make the molecule grow by one molecular unit whenever you click on one of the grey bonds with a purple end, but the screen will not auto zoom if you choose to grow using the GUI method

p:...but you can use the command line <c>grow</c> which will make the molecule grow by one each time the command is entered and the screen will auto zoom
c:mode off
c:grow
c:html.setstate(GROW_SHORT,false)
c:refresh

p:To return the model back to a single molecule simply click on the tab <b>Symmetry Tools</b> then click on the button <b>Fuse</b> or you could simply type in the command <c>fuse</c>
h:h3-h3-symmetry-tools
c:itemstate h3-symmetry-tools 1
h:button-fuse
c:fuse
c:refresh

p:The next mode to look at is <b>Selection</b> which will require you to select an atom before you click the <b>Grow Mode</b> button and then when you select a bond another molecule will be generated from the position of the selected atom.
c:itemstate h3-symmetry-tools 2
c:html.setbg(GROW_SELECTION,red)
c:html.setstate(GROW_SELECTION,true)
c:sel N3
c:run(mode grow GetData(GROW_SHORT) GetData(GROW_SELECTION) GetData(GROW_VDW))

p:You can also use command lines for this mode as well simply select an atom in the structure or use the command line <c>sel [atom]</c> and then enter in the command <c>mode grow -r</c>
c:mode grow -r

p:Selecting a grey and purple bond will then cause the structure to grow using the selection mode.
c:sgen 1+X,+Y,+Z
c:mode off
c:zoom(-0.052994)
c:html.setstate(GROW_SELECTION,false)
c:html.setbg(GROW_SELECTION,lightgrey)
c:rota y 90

p:Another mode you can use is the <b>VdW (Van der Waal)</b> which will show weak intermolecular forces occurring within the molecules you do this by selecting the box
c:fuse
c:html.setbg(GROW_VDW,red)
c:html.setstate(GROW_VDW,true)

p:And again click the <b>Grow Mode</b> button
c:run(mode grow GetData(GROW_SHORT) GetData(GROW_SELECTION) GetData(GROW_VDW))

p:You can now, using the grey and purple bonds, grow another molecule that has a weak interaction with the current model.
c:sgen 3-X,-Y,,2-Z
c:zoom(-0.045)

p:There is also another grow command that doesn't appear on the GUI which allows you to grow a molecule atom by atom as opposed to growing an entire molecule straight away.
c:mode off
c:fuse
c:mpln -n
c:html.setstate(GROW_VDW,false)
c:itemstate h3-growing 2
c:itemstate view-symmetry-generation 2

p:In order to do this you need to enter in the command <c>grow -s</c> then using the up key on the keyboard you can keep repeating the command quickly rather than having to keep typing it out.
c:grow -s

p:The camera should still auto zoom since you are using a command and not the GUI
c:grow -s

p:And again fuse can be used in order to revert back to a single molecule.
c:fuse

p:End of tutorial, press next to repeat the tutorial or cancel to exit.