Chime Features Demo with ATP
To alter the above display*, try the following three types of
Click-and-hold the mouse on the ATP model. From the pop-up menu that appears:
Move the mouse while clicking-and-holding.
- Choose Rotation and select Stop.
- Choose Display and pick one of the following:
- Wireframe shows the connections between (color-coded) atoms;
- Sticks does the same as wireframe, but with thicker connectors;
- Ball & Stick adds spheres to the positions occupied by each atom; and
- 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.
Chime Viewer's Guide provides an outline
summary of the above mouse and keyboard controls.
- 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.
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:
- more than one molecule per PDB file;
- fictitious "temperature" values for some coloring schemes;
- 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 ChimeOptions
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
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.
These pages were made on a PowerMac 7100 with 17" monitor. They also display well
(albeit slowly) on a MacIIcx with 13" monitor (full screen).
Back to Molecular Models for Biochemistry at CMU.
William McClure, MI-646, x8-3430;
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213