PDB Molecules

Using the Chime Plug in
updated 18/01/01

The chime plugin program is called ch203w32.exe is available on iImmunology Website. To install it on your hard drive you first download the program from the RESOURCES section of the immunology website (ie class notes>> immunology>> Resources>> Chime>>ch203w32.exe). Follow the installation instructions

Alternatively, you can connect to the Chime site to download their Plugins

Click on the name of a molecule to view the molecule using the Chemscape^TM Chime^TM plug-in. The default Chime^TM display format is "wireframe" but you can use the mouse to change this to another view (e.g. "spacefill" or "ball-and-stick"). See the Overview page for details about the Chime^TM plug-in.

Running both a browser and helper application at the same time (e.g., both Netscape and RasMol) may require significant application memory (RAM). If you experience system difficulties while trying to run both applications, you may need to install additional RAM on your computer.

PDB Web Sites

Additional PDB molecules can be found at the following sites:

Site name: Brookhaven National Laboratory, Protein Database
URL: http://www.rcsb.org/pdb/

Site name: National Institute of Health, Molecules-R-Us
URL: http://molbio.info.nih.gov/doc/mrus/mol_r_us.html

Web browser software

It is recommended that you use the most recent version of Web browser software that is available. Below are links for both the Microsoft Internet Explorer and the Netscape Navigator software. JavaScript has been an integral part of the Netscape browser for some time; however, only more recent versions of Internet Explorer (i.e., 3.01 and later) include this capability. While the files will function without this enhanced capability, certain actions, such as opening a display window, will work best if you are using a browser that supports JavaScript.

Netscape Navigator: This link will take you to the Netscape Web site where you can download the browser software appropriate for your computer system.
Microsoft Internet Explorer: This link will take you to the Microsoft Web site where you can download the browser software appropriate for your computer system.

Overview

Selected molecules from the textbook are also available in PDB format. You can view and manipulate these molecules within your browser using the Chemscape^TM Chime^TM plug-in from MDL Information Systems, Inc. (see below) or from within various third-party applications such as WebLab Viewer, from Molecular Simulations, Inc. (MSI), RasMol, by Eric Martz at the University of Massachusetts, ChemDraw^TM/ChemDraw 3D^TM, from CambridgeSoft Corporation, or MacMolecule2/ PCMolecule2 from Molecular Ventures, Inc.. PDB files have file names ending in ".PDB". We have included the WebLab Viewer 2.0 application from Molecular Simulations, Inc. Installers for WebLab Viewer can be found in the WLV_PPC directory (for PowerMacintosh systems) and the WLV_W95 directory (Windows '95 systems). Applications for 68k Macintosh and Windows 3.x machines were not available when this CD was produced. However, you can visit the Molecular Simulations Homepage (http://www.msi.com/) for information on availability of the Viewer application for these platforms.

Plug-ins

The PDB files require a special plug-in for your browser in order to display properly.

MDL Information Systems, Inc. Chemscape Chime^TM: The Chime^TM plug-in for Netscape Navigator is required for displaying the PDB files within your Web browser application. MDL recommends using Netscape Navigator 3.01 or greater. Note that Microsoft's Internet Explorer (under Windows 95 and NT) can use the Chemscape Chime plug-in and can render the molecular structures. However, Internet Explorer (under Windows 95 and NT) will not support any Chime scripting. Installers for the Chime^TM plug-in can be found the INSTALL (PC) or INSTALLERS (Macintosh) directory on the CD. Windows 3.1 users should install the 16-bit version of the Chime^TM plug-in (CHI10W16.EXE); Windows '95/NT users should install the 32-bit version (CHI10W32.EXE). The latest versions can also be obtained from the MDL Website. MDL maintains a Chime FAQ if you would like to review some Frequently Asked Questions regarding the Chemscape Chime^TM plug-in.

Chime^TM Instructions

Following are brief instructions on how to manipulate the molecules (PDB format) using the Chemscape Chime^TM plug-in (Macintosh indicated by "MAC"; PC indicated by "PC"):

To open the options menu:

(MAC) - Click and hold down the mouse button without moving the mouse when the pointer is over the image.

(PC) - Click and hold down the right mouse button without moving the mouse when the pointer is over the image.

Options allow the user to:

Change the display type
Change the display options
Change the display color
Bring up an "About" box
Turn on and off molecule rotation
Turn on and off animation
Render molecule files as either 2D or 3D
Store the input file locally

To rotate X- (vertical) or Y-axis (horizontal):

(MAC) - Click and hold down the mouse button while moving the cursor over the image.

(PC) - Click and hold down the left mouse button while moving the cursor over the image.

Note: Movements left-to-right are along the Y-axis; movements up-and-down are along the X-axis.

To rotate Z-axis (orthogonal):

(MAC) - Click and hold the "shift" key, the "command" key and the mouse button down while moving the cursor over the image.

(PC) - Click and hold the "shift" key and the right mouse button down while moving the cursor over the image.

Note: Movements right-to-left are along the Z-axis.

To translate X- or Y-axis (lateral or vertical):

(MAC) - Click and hold the "command" key and the mouse button down while moving the cursor over the image.

(PC) - Click and hold the "control" key and the right mouse button down while moving the cursor over the image.

To zoom or unzoom:

(MAC) - Click and hold the "shift" key and the mouse button down while moving the cursor over the image.

(PC) - Click and hold the "shift" key and the left mouse button down while moving the cursor over the image.

Note: Movements up and down zoom and unzoom, respectively.

Further information about the Chemscape Chime^TM plug-in can be found on the Web pages of Eric Martz, University of Massachusetts, Amherst: "Chime^TM Resources" or "Chime^TM: How To Use It"