Chapter 2-Adding a unit

• The Unit menu-This is a menu of the first ten units in the unit library. An entry in the "Unit Choice" field will be used preferentially over a "Unit menu" entry.
• Type menu-This is used to determine the type of the helix being generated. "A","B", and "Z" are the possible choices. When one is selected the unit parameters will adjust accordingly. B-type helix is the default.
• Unit Choice field-This is used to access units that are not in the unit menu. An entry here is used preferentially to the "Unit menu".
• Dx field-This field allows the user to specify the shift of the unit.
• Dy field-This field allows the user to specify the slide of the unit.
• Dz field-This field allows the user to specify the rise of the unit.
• Tilt field-This field allows the user to specify the tilt of the unit.
• Roll field-This field allows the user to specify the roll of the unit.
• Twist field-This field allows the user to specify the twist of the unit.
• Helix field-This field allows the user to pick which helix the unit is added to.
• Unit field-Allows the user to pick the location in a given helix to insert the unit.
• Attach field- This field tells the program how to make the backbone connection. This takes a M:C:G specifier for each base in the unit. The specifier will be the group(s) that occupy that space in the helix prior to insertion.
• Strand field-This is used to specify the strand direction. "0" indicates 5'->3'. "1" indicates 3'->5'
• Apply button-This executes the operation as specified.
• Quit button-This closes the "Add unit" popup.

Examples

Making an anti-parallel helix

1. Start NAMOT2 and raise the "Add unit" popup
2. Pick a unit from the Unit menu. (e.g.,"a-t-wc").
3. Pick a form from the Form menu. (e.g, the default B-type).
4. Click over apply. The unit should appear in the main window.
5. Repeat steps 2 through 4 to continue adding units to the helix.
See figure 2.1

Making a parallel stranded helix.(I)

1. Start NAMOT2 and raise the "Add unit" popup
2. Pick "ta-rwc" from the "Unit" menu.
3. Choose a form from the "Type" menu.
4. Since this unit is by default parallel, no other change is needed, enter Apply and continue as desired.
See figure 2.2

Making a parallel stranded helix.(II)

1. Start NAMOT2 and raise the "Add unit" popup
2. Pick a Watson-Crick unit from the menu.
3. Choose a form from the "Type" menu.
4. In the strand field, enter "1 1"
5. Click on apply twice in order to produce a 2 unit helix.
6. In this particular case the, the backbone connections are not possible with the default sugar orientations. To correct this
   
   1. Click on the first sugar with the leftmost mouse button
   2. Click on the ending sugar with the middle button.
   3. Choose "chi" from the Sugar controls menu.
   4. Enter 180 in the amount field and press return.
   This should allow the backbone connection to be made.
See figure 2.3

Inserting a unit into a pre-existing helix.

NAMOT2 allows the user to place a unit into a pre-existing helix. An example of this is below.
1. Create a duplex as in the first example.
2. Select a different unit so you can locate the change, I suggest using the complementary pair.
3. Chose helix 1 and unit 2.
4. Enter the attachments. For a 4 unit polymer, these will be "1:1:2 1:2:3"
5. Click on "Apply".
See figure 2.4