AntigenMap 3D Manual. Systems Biology Laboratory. Dept. of Basic Sciences CVM-MSU

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Leslie Eaton
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1 AntigenMap 3D Manual Systems Biology Laboratory Dept. of Basic Sciences CVM-MSU February 3, 2012

2 Contents 1 Quick Start Loading Data Using the 3D Map The Menu Input Format 8 3 Example Usage View a group(s) of antigens Measure distance between two antigens Export a screenshot

3 1 Quick Start AntigenMap 3D is a three dimensional antigenic cartography tool with many built in analysis tools. This section will give a quick introduction on how to use AntigenMap 3D and an overview of the major features. Figure 1 shows an example of the AntigenMap 3D interface. Figure 1: The AntigenMap 3D web interface 1.1 Loading Data 1. Figure 2 shows the start of any AntigenMap 3D run; fill in the form as shown in Figure 3 and click submit. 2. After processing antigen coloring is possible, Figure?? shows the start 2

Figure 2: The starting form of color selection. Use the color picker to select colors for antigen groups. Click the submit button to proceed to the 3D

4 Figure 2: The starting form of color selection. Use the color picker to select colors for antigen groups. Click the submit button to proceed to the 3D map. 3. The java applet will ask permission to run Figure 5, click run to continue loading the map. Figure 6 shows a loaded 3D antigen map that a user can view and manipulate or save for later use. 3

5 Figure 3: The filled in form 1.2 Using the 3D Map Figure 4: The color selection form 4

6 Figure 5: The Java Applet security window Figure 6: The AntigenMap 3D web interface Basic navigation Left-click and drag to rotate the map Use the scroll wheel or SHIFT drag the mouse to zoom 5

7 1.3 The Menu The Menu Right click to open the menu Select shows the number of currently selected antigens Display Selected toggles display of unselected antigens All Selects all antigens None Clears all selections Invert Selection selects the currently unselected antigens and unselects the currently selected ones Set Selection Selection methods Off disables click to select Set Center Sets the center rotation point the the clicked antigen Label On/Off Toggles display of labels for selected antigens Select Antigen Sets selection of individual antigens by mouse clicking Select Group Sets selection to groups of antigens View Default views ( default: front ) Style Adjusts the style of display Perspective Depth Toggles drawing farther away antigens smaller Boundbox Toggles display of the bounding box Axes Toggles display of the X, Y, and Z axes Sterographic Options for 3D displays Labels Labeling options for antigens No Labels Hides the display of labels for antigens With Antigen Name Displays the names of antigens as labels ( on by default ) Axes Display options for the axes Boundbox Display options for the bounding box 6

8 Color coloring options Labels Color options for labels Antigens Color options for antigens Make Opaque Render antigens in solid colors Make Translucent Render antigens in semi-transparent colors by Antigen Group Color antigens by group ( default ) by Antigen Number Color antigen uniquely Axes Changes the color of the axes Boundbox Changes the color of the bounding box Background Changes the color of the background ( default: black ) Zoom Zoom options Spin Enables/Disables automatic spinning of the map Measurements Options for measuring antigenic distance Show Measurements Toggles display of measurements Click for Distance Measurements Enable single clicking to measure between two antigens Clean Measurements Remove all previous measurements List Measurements Displays a list of all current measurements Save Saving options File Saves the 3D coordinates of the antigen map JPG Image Saves the current view as a JPEG image PNG Image Saves the current view as a PNG image POV-Ray Image Exports the current view for rendering in POV-Ray Language Changes the language of the menu ( note some items may not have translations ) Console Opens the Jmol console for advanced usage 7

9 2 Input Format The Input format is a tab delimited data format exportable from a spreadsheet ( an example sheet is available online ). The first row of data lists the number of antigens and the number of antisera. The second row contains the column headers and the antisera names. The third row contains the reference numbers used in normalization methods 4 and 5. The rest of the rows are the antigen names and groups followed by their HI data. Example: num. antigens num. antisera ID Group antisera1 antisera2 Reference antigen1 G antigen2 G antigen3 G Example Usage 3.1 View a group(s) of antigens 1. Menu Select None 2. Menu Set Selection Select Group 3. Left click on the group(s) 4. Menu Select Display Selected 3.2 Measure distance between two antigens 1. Menu Measurements Click for Distance Measurements 2. Left click on the two antigens 3. Repeat for all required measurements 4. Menu Measurements List Measurements 8

10 3.3 Export a screenshot 1. Setup the window as you want the screenshot to appear 2. Menu Save JPG Image 3. Save dialogue opens for screenshot 9

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