MarvinView Example - XYZ animations

In this example a molecular dynamic simulation is shown about the thermal motion of a segment of a protein alpha helix. The simulation is provided by Raul E. Cachau <cachau@ncifcrf.gov>.

The animSync parameter is used to synchronize the animation in the two cells. The spin1 parameter sets the spinning rate and axis for the right cell.

<script type="text/javascript" SRC="../../../marvin.js"></script>
<script type="text/javascript">
<!--

mview_begin("../../..", 561, 300);
mview_param("molbg", "#000000");
mview_param("atomSymbolsVisible", "false");
mview_param("animSync", "true");
mview_param("spin1", "30,1,-1,0");
mview_param("navmode", "rot3d");
mview_param("rendering", "spacefill");
mview_param("rows", "1");
mview_param("cols", "2");
mview_param("border", "1");
mview_param("layout", ":2:1:M:1:0:1:1:L:0:0:1:1:c:n:1:1");
mview_param("param", ":M:280:280:L:10b");
mview_param("cell0", ":../../../mols-3d/all_atoms_cyclic_traj.xyz.gz:All atoms");
mview_param("cell1", ":../../../mols-3d/backbone_atoms_cyclic_traj.xyz.gz:Backbone atoms only");
mview_end();

//-->
</script>

Note, that this animation does not work in Netscape versions earlier than 4.0 because Java 1.1 is needed for unpacking the gzipped files.

Description of the used parameters:

• animSync
• spin1
• navmode
• rendering

 

The next example shows how to visualize chirality in the viewer.