In the previous tutorials you worked with one file type at a time – either a Construct window or a Gel window. However, when you are designing a cloning strategy it is often desirable to include many different constructs and gels in the same document along with descriptive text. This is the function of the Illustration window. This tutorial is designed to give you a general idea of what the Illustration window can be used for.

1. Start GCK and open the file construct#5 , which is in the tutorial files folder. This is the vector we will use in our cloning project.
2. Click in the construct and choose Edit > Select All and then choose Edit > Copy to copy the entire construct to the clipboard.
3. Choose File > New… and choose to create a new Illustration window by clicking the Illustration radio button (see the dialog in Figure 2.49). Name the new window “ cloning project ” and press OK. A new Illustration will be created.
4. In the new window you should see a blinking cursor that represents the top left corner of whatever you choose to paste into the window. Click the mouse about 3 cm from the top and 3 cm from the left and then choose Edit > Paste . This will paste construct#5 into the Illustration window. You might want to make the window larger at this time to be able to see what is going on.
5. Notice that the pasted construct now has 8 handles (little square filled boxes) around its edges, indicating that you can drag it around the window and resize it. Also notice, there is now an Illustration menu in the menu bar because an Illustration window is the active window. Choose Illustration > Set Construct Scale… and enter 300 into the dialog as shown in Figure 2.52. Press the OK button. The set scale option in the Illustration window allows you to make sure that all of the constructs in any given Illustration are all drawn to the exact scale you desire. This operation will make your construct look a little ugly – the title will be too big for the construct and the arrowheads and line thickness for the orange region in the middle will be too large. They need to be fixed.

   Figure 2.52: Set Construct Scale…

6. One of the most powerful features of the Illustration window is that objects can be edited as if they were in their own windows. To access the editing, simply double-click on the construct#5 – this is called making the object a target, or targeting an object. Target construct#5 now. Note that there is now a Construct menu in the menu bar in addition to the Illustration menu. Click on the construct title and drag it below the circle. Adjust the line thickness and arrowhead size for the orange region by using Format > Lines >. If region names are shown, hide them using Format > Regions > Hide Region Names. You should try to get something that looks like Figure 2.53.

   Figure 2.53: Illustration#1

7. Now let’s put a title in the illustration. Click on the “ T ” icon in the lower left corner of the Illustration window to activate the Text tool. Click the mouse near the top left corner of the Illustration window. You will see a blinking insertion point. Before you type anything you need to set the font and font size. Using the Format menu, choose Arial as the font and set the font size to 24. Now type “An Important Cloning Project”. Don’t worry about the appearance of the text for now – we will fix it in the next step.
8. What you will see is large letters of text overwriting the construct. To fix this you need to adjust the size of the text object you just created. You are currently editing the text within the text object (it is targeted) but you want to be able to resize the text object as a whole. This is similar to being in the mode of editing a construct (as you just were) and wanting to change the size of the construct. What you need to do is deselect the text object by clicking in a blank area of the Illustration window, and then select the text object by clicking once on it. This will give you the eight handles around the object. Use the top right handle to drag the right edge of the text object towards the right edge of the window. You will end up with something like Figure 2.54.

   Figure 2.54: Illustration#2

9. Open the file hsp70 , which is in the tutorial files folder. Mark all the BamHI sites as you did in Tutorial 2: Marking Sites (there should be three sites).
10. Click once in the hsp70 DNA and then press command-A/ctrl-A (or choose Edit > Select All) to select the entire construct. Copy this construct to the clipboard by pressing command-C/ctrl-C (or choose Edit > Copy).
11. Bring the Illustration window to the front by clicking on it or by using the Window menu. Click the mouse to the right of construct#5 and paste (Edit > Paste). This construct is much too large to fit on this page, so choose Illustration > Set Construct Scale… and set the scale to 800 nts/cm . You should have a figure that looks like Figure 2.55.

    Figure 2.55: Illustration#3

12. Now open the file hsp70(Bam-). Select the entire construct, copy it, and paste it below the hsp70 construct in the Illustration window. As you did in the last step, set the scale of this construct to 800 nts/cm.
13. We want to indicate in the Illustration what was done to get from hsp70 to hsp70(Bam-) . To do this, we need to type in some descriptive text between these two constructs. To make room for this text, you first need to move the construct title for hsp70 to the top of the construct itself (we are creating Figure 2.56 if you want to look ahead). Double-click on the hsp70 construct to make it the target and then drag the construct title above the DNA.
14. Now click on the “T” tool again in the bottom left corner of the window so that you can enter your description of the procedure. Click between the two linear constructs (you will get a blinking insertion point) and set the font to Arial 9 point plain text using the Format menu. Type in a description of the step used to modify hsp70 .

    Figure 2.56: Illustration#4

15. Click on the arrow tool (the third tool from the left) in the bottom left corner of the Illustration window and draw a vertical arrow from top to bottom as shown in Figure 2.56.
16. We now need to create a legend for the site marker symbols in construct#5 . Double-click on construct#5 to make it the target. Now click on one of the site markers and press command-A/ctrl-A ( Edit > Select All ) to select them all. Hold down the shift key and click on the BamHI marker to deselect it. Choose command-C/ctrl-C ( Edit > Copy ) to copy all the sites to the clipboard.
17. Click in the Illustration window under construct#5 and paste the site markers into the window ( command-V/ctrl-V ). Drag the legend you just created to the left of construct#5 making it look like Figure 2.57.

    Figure 2.57: Illustration#5

18. There are many more steps to complete this project but you should get the flavor of the Illustration window by this time. You can open the file cloning project in the tutorial files folder to see what the final illustration might look like. Feel free to explore the completed illustration to learn some other tricks. Notice also that you can copy the gel lanes and paste them into the Illustration window to complement the other information in that window. The Sample Files folder also contains some interesting examples.

This concludes this tutorial. Close all the open windows, but please don’t save changes to any of the tutorial files provided with the program so that others can do the tutorials in the future.