3D View

Help & Reference

Three-dimensional View

The three-dimensional views now employ JSmol, replacing the Jmol java applet used previously. JSmol uses JavaScript and HTML5, and has major advantages over Java in terms of users not having to adjust their security settings and being able to view the graphics on the iPad or iPhone. However, performance is a little slower than the original Java applet.

Off-line viewing

Some users may wish to view motifs off-line in their own preferred desktop molecular-graphics application. (There are several free programs of this type — e.g. RasMol and PyMol, in addition to the Jmol application — as well as commercial products.) In this regard it should be pointed out that the single-subunit structure files used here (further edited in some cases) can be downloaded from the Jmol applet window using the pop-up menu accessed from the ‘Jmol’ logo. Select the protein PDB designation (e.g. 119L) from the top of the menu, and then the (non-standard) PDB filename (e.g. 119lH.pdb) at the bottom of the sub-menu, and the download should start.