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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 how to use the Illustration window.
1. Start GCK and open the file construct#5, in the tutorial files folder.
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 create a new Illustration window by clicking the Illustration button. Name the new window 'cloning project' and press OK.
4. In the new window you will 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.
5. Notice that the pasted construct now has 8 handles (little square filled boxes) around its edges, indicating that you can drag it and resize it. Choose Illustration > Set Construct Scale... and enter 300 into the dialog. 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 magenta region in the middle will be too large. They need to be fixed.
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Figure 45: Illustration#1
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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, double-click on construct#5 - this is called making the object a target. 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 magenta region by using Format > Lines >. If region names are shown, hide them using Format > Regions > Hide Region Names. You should get something like Figure 45.
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. Using the Format menu, choose Times as the font and set the font size to 36. Now type 'An Important Cloning Project'.
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Figure 46: Illustration#2
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8. You will see is large letters of text overwriting the construct. To fix this, the size of the text object needs to be adjusted. 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. What you need to do is deselect the text object by clicking in a blank area of the window, and then select the text object by clicking once on it. This will give you the 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 should have something like Figure 46.
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 (Mac) or Ctrl-A (Windows) to select the entire construct. Copy this construct to the clipboard by pressing command-C (Mac), Ctrl-C (Windows).
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Figure 47: Illustration#3
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11. Bring the Illustration window to the front by clicking on it. Click the mouse to the right of construct#5 and paste (command-V, Mac; Ctrl-V, Windows). 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 something like Figure 47.
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.
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Figure 48: Illustration#4
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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 descriptive text between these two constructs. To make room for this text, you need to move the construct title for hsp70 to the top of the construct itself (see Figure 48). Double-click to target the hsp70 construct and move the construct title above the DNA.
14. Now click on the T tool in the bottom left corner of the window. Click between the two linear constructs (you will get a blinking insertion point) and set the font to Geneva/Arial 9 point plain text using the Format menu. Type in a description of the step used to modify hsp70.
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 the top to bottom hsp70(BamHI-) construct as shown in Figure 48.
16. We now need to create a legend for the site markers in construct#5. Double-click on construct#5 to target it. Click on one of the site markers and press command-A (Mac) or Ctrl-A (Windows) to select them all. Hold down the shift key and click on the BamHI marker to deselect it. Choose command-C (Mac) or Ctrl-C (Windows) to copy all the sites to the clipboard.
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Figure 49: Illustration#5
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17. Click in the Illustration window below construct#5 and paste the site markers into the Illustration by pressing command-V (Mac) or Ctrl-V (Windows). Drag the legend you just created to the left of construct#5 to make it look like Figure 49.
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.
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