Indiana University Bloomington
IUMSC   Indiana University Molecular Structure Center

Data in the Reciprocal Net system consist of two distinct sections. The structural results are located in a data repository on the server, and a database is available to locate data in this repository. The contents of the repository generally include a "Crystallographic Information File" (CIF) which contains most of the important crystallographic information for the structure. In addition there are normally several other files present that allow the user to view the molecule using the web interface.

Crystallographic data for a molecular structure consists of a set of atomic coordinates for each unique atom in the crystal, the identity of the particular element, and information on the symmetry present in the crystal. The coordinate data can be expressed in several forms, including crystallographic coordinates and Cartesian coordinates.

The symmetry information includes translational symmetry as well as various point and plane symmetry elements. In some cases molecular symmetry will be present, and symmetry operations are needed to generate a complete set of atomic coordinates for the molecule. For most of the graphics used in the IUMSC server a complete molecule has been generated.

When the user goes to the data entry page for the structure of interest, a page similar to the following will appear:

data entry page (Click to see an enlarged image)

miniJaMM applet

Most of the information above is self-explanatory. The miniJaMM applet is somewhat limited in capabilities, but can be used to rotate and examine the structure.

Because of its simplicity, the miniJaMM link offers the fastest download of the JaMM series applets. It will show a simple stick image of the molecule that is color coded for the types of atoms present, and can be rotated by depressing the left mouse button while dragging the cursor in the applet window. The right button will resize the molecule in a similar manner. Three other commands are available by depressing keys on the keyboard:

"l"label atoms
"h"label hydrogen atoms as well
"r"reset drawing
"a"show combined rotation angles
"?" list help screen

JaMM 2 applet

The JaMM 2 applet (click on the JaMM 2 link below the applet) is the most versatile of the applets currently supported. The JaMM 1 applet is still available to support older browsers and should only be used if your browser does not support the JaMM 2 applet. A view of the JaMM 2 applet is shown in the left side.

The top section allows you to choose between line drawings, ball and stick, or space filling representations.

The second section allows you to specify monographic or stereographic representation.

The third section allows you to identify atoms, determine bond distances, and bond angles in the image.

Other options include labeling, showing the rotation angles, and whether or not the hydrogen atoms should be shown. The Line Drawing, ORTEP Diagram and Rendered Image options are explained below.

The bottom of the applet is the text window which lists alphanumeric output as required by the other options.

When the Line Drawing or ORTEP Diagram button is selected, the applet submits an instruction stream to server-based programs that will generated publication quality results. The results are returned in a separate window, and include a .jpg image of the molecule as well as links to a PostScript file for the image and the input deck that was used to generate the ORTEP drawing. The following shows the line drawing and ORTEP images for the above molecule.

line drawing image of molecule

ORTEP image of molecule

The Rendered Image button creates a ray traced image file request that is submitted to the IUMSC Beowulf system for high resolution rendering. The following describes the input necessary for the ray traced image:

rendering options

The image generated will correspond to the image type selected in the JaMM 2 applet. Line Drawing will yield a stick drawing, the Ball and Stick option will yield an image that appears to be made of plastic balls and aluminum rods, and the Space Filled option will create an image with intersecting spheres representing the atomic radius. The ball size value can be changed to be a fraction of the "normal" to oversized diameters. The Image Size is the number of bits in the x and y direction for the final image. The user can change the background color in the applet (and in the final image generated) by changing the values for red/green/blue using the slider bars or directly entering the numeric values. When Close is selected, the values will be maintained until the user leaves the JaMM 2 page.

Space Filled image of the molecule

By selecting Space Filled in the applet and selecting "render on white background" the following image is generated.

Note that the bottom part of the page has a section titled Repository Files:. This section contains a list of the files that have been placed in the repository by the crystallographer who performed the analysis. The actual content of this section will vary depending on the personal tastes, as well as the availability of information for some structures.For a complete explanation of the files that are available in the data directories, visit the What Data Will I Find? page.

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