Chime Features Demo with ATP

     To alter the above display*, try the following three types of manipulations:
  1. Click-and-hold the mouse on the ATP model. From the pop-up menu that appears:
    • Choose Rotation and select Stop.
    • Choose Display and pick one of the following:
      1. Wireframe shows the connections between (color-coded) atoms;
      2. Sticks does the same as wireframe, but with thicker connectors;
      3. Ball & Stick adds spheres to the positions occupied by each atom; and
      4. Spacefill and then Van der Waals Radii corresponds to the van der Waals surface of the molecule.
    • Choose Options or Color and make some choices. Except for the CPK choice, the features in these lists are more relevant for macromolecules. However, if you prefer to view Spacefill models with Specular and Shadows applied, instead of the standard Ball & Stick display used here, those options are available.
  2. Move the mouse while clicking-and-holding.
    • This action will rotate the model about its axes.
    • Repeat with the "shift" key held down to zoom in and out.
    • Repeat with the "command" key held down to translate in X or Y directions.
  3. Click on this button to display a labelled version of the different parts of ATP.

    4. Chime buttons launch prepared RasMol-like scripts that perform actions on the model. (In this case a fictitious "Temperature" Color was used to highlight the model as shown.)
    Choose CPK again under Color to get back to the standard display. Well, almost standard, but the labels are still there. Reload this page to get back to the original display. For the other pages that use Chime buttons, Reload Frame under the NETSCAPE View menu will restore the starting image.
    Reload Frame can also be used when a button or image fails to appear on first loading.
The Chime Viewer's Guide provides an outline summary of the basic mouse and keyboard controls.
The CMU Chime Tutorial, written by Dr. Gordon Rule, takes you through most of the features of the Chime 2.0 menu selections.

Go to the Chime & RasMol Command Line page to examine some features of Chime displays of proteins.

Some technical details.
Unless otherwise noted, the small molecule atomic coordinates are from Klotho. In all cases the XYZ coordinates were converted to RasMol 2.6 PDB files. They were then edited to provide correct CONECT-line information for Chime. In some cases, the PDB files were further altered to include:

  1. more than one molecule per PDB file; 
  2. fictitious "temperature" values for some coloring schemes;
  3. fictitious residue numbers ("resno") for RasMol selection of portions of a molecule.


Displays of single and double bonds.
Wireframe double bonds can be displayed from a selection under the Chime Options menu.
The only double bonds displayed on these pages are those that have complete double bond character. Bonds included in this category are: 

  • -C=O in aldehydes, ketones, esters, and amides;
  • -C=C- in fumarate, cisAconitate, etc.
Represented as single bonds are those in: 
  • aromatic rings systems;
  • carboxylate groups; and 
  • other conjugated species (e.g. guanidino of Arg).


These are shown as single bonds because the Klotho coordinates show them to be of equal length. Hence, their partial double bond character is not displayed.

*If you see one of those annoying NETSCAPE "broken image" icons instead of a beautiful ATP molecule, try checking the function of your Chime plug-in on the standard images at the MDL Inc. site.
If image loading is an intermittent problem, try :

  • increasing the Netscape memory allotment, eg. 15 MB;
  • clearing the Netscape cache (under "Options", "Network Preferences...");
  • or restarting Netscape.
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William McClure, MI-646, x8-3430;
wm0p@andrew.cmu.edu.
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213