Circular Maps

To open the Circular Map for a circular sequence press 'Map' and select 'Circular' or use the menu option 'Vector' -> 'Circular Map'.



There are 5 control panels, 'Enzymes', 'Appearance', 'Save/Print', 'Hints', 'Element'

'Enzymes' panel

You can add 'groups' of enzymes to the map using the buttons in the 'Add groups and layout' panel. eg press 'unique prototypes', then the 'layout' button.

You can edit the layout of enzymes on the map manually by clicking and dragging enzymes to the desired position with the mouse. Shift-click and drag to reposition the name text relative to the location line

Right click an enzyme on the map for a pop up options menu including 'remove' and 'colour'

You can also Add/Remove individual enzymes from the map from the table of enzymes

'Multiple Cloning Site Controls'

Annotations or Vector Elements that are designated as MCSs can effect how enzymes sites are displayed on circular maps. Select 'separate' on the '(MCS) controls' on the enzymes panel to display sites that fall within the MCS annotation in an aligned list, as in the illustration above. 'fix position' orientates the MCS at 3 o'clock on the display. 'details' adds a text version of the mcs to the map itself. You can opt to include a translation and set it's frame. You can drag the 'text mcs' on the map to re-position it.

The enzymes that the program chooses to display are those that have non-degenerate recognition sequences or are in enzyme box 'commonMCS' and that cut once or twice within the designated MCS Element.

You can press the 'Set MCS' button to create a new MCS vector element if one is not already defined for the sequence

'Appearance' panel



You can draw 'annotations' and/or 'vector elements' on the circular map, as determined by the checkboxes in the 'include' panel. This panel also has checkboxes to include a text list of the annotations/elements and a text list of absent restriction sites. Note that you can re-position the text lists on the map by draging them with the mouse.

Adjusting the Maps Size and Position

You can adjust the maps size and position using controls on the 'Size/Position' control panel. Adjust each slider to give the desired 'Horizontal' and 'Vertical' position and 'Radius' and 'Rotation'. You can adjust the offset and width of all the annotations/elements. If a MCS Element is present, you can adjust the offset of it's enzyme list.

You can adjust the font for the enzymes and annotations on the map using the 'font' controls You can add additional text to the map by pressing the 'Add New Text' button. Pressing this button adds the text 'New Text' to the top left of the map. Note that you can now edit this text, drag it to the desired position, and right click it for a pop up options menu where you can adjust the font, or delete it.

'Elements' panel


If you select an element by clicking it on the maps circular graphic sequence line, an editor panel for the element appears in the right hand side control panel.

You can also add a new element by pressing the 'Add New Element' button

The text that represent the Elements 'Value' (eg Ampicillin) is displayed on the map within each element if there is space. If no text is present for a particular element it is likely that the text is to long to fit inside the element. In the case of 'Ampicillin' shortening the text to 'Amp' for example or decreasing the texts size using the pop-up menu 'Text Size' option could be used to make the text displayable. The width and offset of elements can be adjusted using the width and offset spinner on the elements control panel

'Save/Print' panel

to keep changes you have made to the circular map, you can either press the 'Retain Changes' in this panel, or confirm 'Retain Changes' when you close the map editor window. If you don't retain changes, any changes made will be lost

*** NOTE that 'retain changes' is not equivalent to 'SAVE' to file. If you also want changes to your circular map to be 'SAVED TO FILE' you must also 'SAVE' the file