PDB/Jmol for 3D Structure Display

26 June 2006

What is PDB ?

PDB means Protein Data Bank format, which can be used for molecular drawing applications such as Jmol. Although Jmol can now accept CIF files, it cannot yet interpret the space group symmetry operations. ICSD-for-WWW therefore produces simple PDB format files that contain a list of all the atoms in the unit cell with their co-ordinates on orthogonal axes.

What is Jmol ?

Jmol is a Java script application for embedding interactive 3D chemical structures within a Web page (cf Chime, Rasmol etc). If you cannot see the famous YBaCuO superconductor structure opposite, you should download and install the Java Runtime Environment JRE. You can use the mouse to manipulate the structure in 3D.

Jmol is an interesting alternative to the usual VRML 3D-display. You can otherwise download the CIF file from the structure "Details" and use eg the free Mercury structure display and CIF editor.
Note:Loading for the first time entails a ~1MByte automatic download; subsequent displays will be much faster.

H3>Mouse control in Jmol

  • Rotation - hold the mouse button down and drag on the structure.
  • Zoom - press the shift key while dragging vertically with the mouse (or drag the middle button).
  • Translate - press the Ctrl+Alt keys while dragging with the mouse.
  • Distances - Double-click an atom, then drag the mouse and click on another atom.
  • Angles - As for distances, then drag the mouse and click on a third atom.
  • Menu Options - press the right mouse button or click on the Jmol logo.
  • Download PDB - select the fileName.pdb option in the first pop-up menu (with pop-ups unblocked).
  • Selecting - eg select an element and uncheck the "poly" or "bonds" box.
  • Console - Open the console option and type Jmol commands into it eg:
        polyhedra off; spacefill 50%; spin on; animation on; (see the the full list of Jmol commands).
    The ICSD database is copyright 2007 by Fachinformationszentrum (FIZ) Karlsruhe (c)2007 FIZ Karlsruhe
    Please report technical problems with ICSD for WWW to hewat@ill.fr (Alan Hewat).