The Construct Menu provides complete control over the appearance of your constructs. You can choose to show or hide certain features of the display and can add regions of interest and marked sites as well.
When viewing a construct graphically, the Magnification Submenu of the Construct Menu will be enabled. Selecting Zoom In will magnify the view and center it about the location of the insertion point. Zoom Out will decrease the magnification. Fit To Window proportions the construct to fit within the window. If Fit To Window is chosen, the construct will be redrawn and rescaled each time the window is resized. With any of the other options, the construct will not be rescaled if the window size is changed. Fit To Printer Page will resize the drawing to fill up a single printed page, as defined in Page Setup under the File Menu.
The Display Submenu has many options, some pertaining only to the sequence view, others to the graphics view, and some to both views. Show as Double/Single Stranded pertains only to the sequence view and allows you to display the sequence as double or single stranded.
Another option available only in the sequence view is Show/Hide Positions. Showing positions will place line numbers at the beginning of each sequence line. It will display the starting nucleotide position of the DNA sequence line and will display the starting amino acid position of the peptide line (if a peptide is visible).
The next item on the menu depends on whether the construct is being viewed graphically or as a sequence. When shown graphically, the menu item reads Show/Hide Scale Legend, which shows a horizontal bar indicating the scale at which the construct is drawn. The scale can be set by double-clicking on the scale legend. Hide Scale Legend will remove the scale legend from view, but will still keep the construct at the same scale. Once the scale is set using this dialog box, resizing the window will not change the scale. To have the construct resize as the window is resized, you need to select the Fit To Window option from the Magnification Submenu.
If the construct is being viewed as a sequence instead of graphically, the Show/Hide Scale Legend menu item will be replaced by Show/Hide Line Borders. Line borders serve a function analogous to the page borders option. They delineate each sequence line from the next.
Set Line Spacing… can be used in the sequence view to set the minimum spacing between adjacent sequence lines. If set to zero, the program will use the correct spacing for the font and style chosen foreach part of the sequence. If a positive number is entered, the adjacent lines will be moved apart by that many pixels in addition to the normal spacing between sequence lines.
The next set of menu commands are self explanatory and allow you to customize the display of the construct to show only the features that you are interested in. Show/Hide Regions, Show/Hide Sites, Show/Hide Comments, and Show/Hide Generations all do what their names suggest.
Once regions have been created, it is sometimes desirable to rearrange them. This can be accomplished using the Move Region to Outside and Move Region to Inside options. Selecting a region and then choosing one of these options will move that region to the designated location. For linear constructs, these items read Move Region to top and Move Region to bottom.
The last item on the Display Submenu is Display Sequence/Display Graphics, which toggles the display of the Construct Window between a graphical representation of the construct and a sequence listing of the construct.
Make Region will create a region of interest corresponding to the selected segment of the construct or sequence. Once created, the region can be selected and then modified using any of the appropriate commands on the Format Menu and can be defined as a coding region by setting the Protein Sequence button in the Get Info… dialog box.
The Mark Sites… menu item allows you to mark specific sites on the construct using sequences entered in a List Window. The Gene Construction Kit will search the construct for the list sequence and place site markers at all locations within the construct that match the sequence chosen from the List Window.
Mark Location… is similar in function to the Mark Sites… menu option in that it will place a marker on the construct. Unlike Mark Sites…, however, Mark Location requires that you type in the exact position for the site marker to be placed and the name for the site marker.
A string of generic nucleotides (Ns) can be inserted into a construct using Insert Ns… from the Construct Menu. Used in conjunction with the Place Sites option (below), complete figures can be made even if your information consists only of the construct size and the locations of some restriction sites.
Insert Typing… is available only in the sequence view of the construct. It can be activated either by selecting it from the menu, or by placing the cursor in the sequence and then starting to type.
Place Sites… provides the opportunity to insert recognition sequences into a construct at specific locations. Using this feature, you can actually place restriction sequences into your DNA at specified locations.
When the cursor is placed at the end of a construct, the Edit Construct End… menu option is enabled. Selecting this menu item will bring up a dialog box similar to the standard ligation dialog box allowing you to edit the DNA end in the standard Gene Construction Kit fashion.
If the cursor is not located at an end in the construct, but is instead at a marked site, the menu changes to Edit Cut Site… and will present you with a dialog box similar to the standard ligation dialog box.
Find Sequence… allows you to search through the DNA for a specific sequence. The Gene Construction Kit will search through the construct and highlight any match with the search sequence.
In the graphical view of a construct, either Redefine Origin or Set Beginning Position will be available. For circular constructs, Redefine Origin will rearrange the construct so that the current position of the insertion point will become the new origin for the construct. For linear constructs, this menu item will define a different number for the initial nucleotide in the sequence using Set Beginning Position.
Get Info… will provide information on any selected object in the Construct Window. You can Get Info… on construct segments, marked sites, or regions. Depending on the object selected, you will get a different but similar dialog box containing information relevant to the selected object.
General Info… differs from Get Info… in that it provides information about the entire construct. General information is attached to the window (file) and will not be lost when segments are cut and pasted within the window. Copying an entire construct and pasting it into a new window will copy the general information. Pasting the entire construct as a segment of another construct will convert the general information into info attached to the new segment that is the result of the paste operation.
The Search Comments… option provides the ability to search through all the comments that are associated with a construct in all generations. General info, segments, regions and/or marked sites can be searched. Matches that are found are listed and comments can then be viewed.
Make Linear/Make Circular is selectable only in the graphics view of a construct and will toggle the graphics view between a linear and a circular construct. When converting from circular to linear, the origin will be the site at which the construct is opened. Conversely, when going from linear to circular, the ends of the linear segment will be joined to become the origin. If the ends are not compatible, you will be presented with a ligation dialog box.
