ICSD for WWW

Help with CIF/Jmol for 3D Structure Display

3 July 2006

What is CIF ?

The CIF format is the standard defined by the IUCr. You are advised to check the CIF file using one of the free CIF syntax checkers e.g. CCDC's free Encifer. You should in particular check the symmetry operations, for example by using CCD's Mercury molecular plotting application. Some journals (eg IUCr's Acta Cryst) publish the original CIF files, and these should be used when available rather than these CIF files re-generated from the ICSD data.

What is PDB ?

PDB means Protein Data Bank format, which can be used for molecular drawing applications such as Jmol. ICSD-for-WWW can produce a simple PDB format file that contains a list of all the atoms in the unit cell with their co-ordinates on orthogonal axes. But normally you should use Jmol to display the CIF file.

What is Jmol ?

Jmol is a Java application for embedding interactive 3D crystal structures within a Web page (cf Chime). If you cannot see this Y₁Ba₂Cu₃O_7-x superconductor structure , you should download and install the Java Runtime Environment JRE. Make sure stay updated with the latest version of JRE. Jmol now displays anisotropic thermal vibration matrices Uij or Bij as in this simple KCaF3 example. (Choose "ellipsoids" as the display. If these are non-positive definite, they are drawn as small squares).

You can use the mouse to manipulate the structure in 3D, display any structure from ICSD, or even display your local CIF, ShelX, PDB etc files downloaded from journals or other databases. Jmol is a powerful alternative to the ICSD VRML 3D-display. Many thanks to Bob Hanson for helping tailor jmol for inorganic structures.
Note: Loading for the first time entails a ~1MByte automatic download; subsequent displays will be faster.
Note: If you have no display, try opening your Java control panel and deleting the java temporary internet files.

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).

Turn - Press the shift key while dragging horizontally 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 double-click a second atom.

Angles - Double-click an atom, click a second atom then double-click a third atom.
Single click an atom to list its name and coordinates at the bottom of the browser window.

Menu Options - Click the right mouse button (or click on the Jmol logo for a shorter menu).

Download file - Select the fileName option in the first pop-up menu (with pop-ups unblocked).

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).

Jmol Window Options

0%,25%,100%,ionic - percentage size of the van der Waals spheres, or else use ionic radii.

bonds - Switch bond drawing ON/OFF within the limits displayed in Å (reload to change these limits).

poly - Switch polyhedra display ON/OFF. This applies to all created polyhedrae for the selected atoms.

label - Label the selected atoms (normally labels all atoms).

persp - Draw the unit cell in perspective (normally no perspective is used).

stereo - Draw a red-cyan stereo pair of views (you will need red-cyan filter glasses).

B/G - Draw the background as black (normal) or white (when unchecked).

Hbonds - Draw dashed hydrogen bonds (normal) or remove them (when unchecked).

anim - Animate i.e. flip through success structures for a multi-structure CIF to compare them.
Create multi-structure CIF files for comparison by simply cocatenating individual CIF files.

cavities - Draw the isosurface of cavities in zeolites and other framework structures.

Advanced Jmol Window Operations

Select - Permits selection of particular atom sites with the mouse (instead of the default "all selected").

Create - Creates bonds and polyhedra around the above selected atom sites within Å distance.

Colour - Colours the selected atoms & polyhedra, includes the default "colour", "transparent" etc.

Å distances - The range of inter-atomic distance for drawing bonds/polyhedra. Changes require a "Reload".

*a,*b,*c - Draw multiple unit cells *a,*b,*c on "Reload". Default is one cell 1,1,1.

Big - Reload the structure in a full-screen window (display multiple cells and use new Å distances).

Reload - Reload the structure in the default small window (display multiple cells and use new Å distances).

Plot a local structure file - Click "Browse" for the file then "Plot" it. Incompatible files will be rejected.
CIF, ShelX, PDB, MOL etc structure files can be plotted, but avoid including unusual characters like "<".

Print - Print the contents of the Jmol window (printing a big window takes some time).

Hints for Constructing New Bonds and Polyhedra

Not all combinations of these options are possible with such a simple interface. Experiment for yourself. eg:

Check "Select" and click on the central Y atom in Y12367, then check "Create". (You should select Y in both frames).

Now uncheck "Select" and check "Select" again (select none) then uncheck "Create" and finally uncheck "Select".
This is to avoid destroying bonds and polyhedra that may be still selected (think about it).

To remove polyhedra, select the central atom (after clicking "poly" to hide all polyhedra if necessary)
then click "Create" twice to first create then destroy these specific polyhedra.
Un-select "Select" and click on "poly" to view all remaining polyhedra.

Or try switching "bonds" off then on, or try reloading with different Å bond limits or multiple cells.

Or open the console and type command: isosurface delete select (oxygen) hkl {1 1 1} ionic molecular;