Animation

A brief introduction to user animation in jV.

Step-1: Minimum Example

To display the animation on the web using jV, you should prepare an animation file and a html file.

step-1

The format of the animation file is the same one as the PDB format of the NMR structure with multiple models. In other words, each frame is separated with MODEL recored. An example animation file can be obtained from here.

The html file, shown below, should contain the applet tag to activate jV and it requires code parameter, codebase parameter and archive parameter. The parameter “code” is a kind of magic word to use jV. The codebase points the relative path to the jV jar file existing from the html file is stored, and archive parameter indicates the name of jar file. The jar file can be obtained from Installation of jV3.

<html><body>
<applet code="org.pdbj.viewer.gui.ViewerApplet"
   codebase="."
   archive="jv3_3.jar"
   width=400 height=400
   <param name="animURL"
       value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdg">
   <param name="commands"
       value="select all;wireframe on;anim forward">
</applet>
</body></html>

Step-2:Make more fancy

step-2

To display cartoon and color from N-terminal to C-terminal in white background,change “wireframe on” to “cartoon on” & add “color group;”

NOTE: As in this example, any jV code (similar to Rasmol script) can be used in the commands parameter. And each jV command should be separated by “;”.
Complete Code until here.

<html><body>
<applet code="org.pdbj.viewer.gui.ViewerApplet"
   codebase="."
   archive="jv3_3.jar"
   width=400 height=400
   <param name="animURL"
       value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb">
   <param name="commands"
       value="background white;select all;background white;
              cartoon on; anim forward">
</applet>
</body></html>

Step-3: Swing & move quick!

To control the speed of animation and the animation mode (shown once, swing, or loop), add two commands, “animmode swing; animspeed 20;” (20 is just an example).

<html><body>
<applet code="org.pdbj.viewer.gui.ViewerApplet"
   codebase="."
   archive="jv3_3.jar"
   width=400 height=400
   <param name="animURL"
       value="http://ef-site.hgc.jp/jV/example/1byi_1-anm.pdb">
   <param name="commands"
       value="background white;select all;background white;
              cartoon on;
              animmode swing;animspeed 20;
              anim forward">
</applet>
</body></html>

Step-4: Advance usage in ProMode

ProMode

ProMode is a database of normal mode analysis of proteins. In the database Animations are provided with jV. You can see the case of 1BYI, which is used as an example of this page.