Chimera Configuration Instructions

There are three steps involved in setting up Chimera on your system to interface with ModBase:
  1. Installing Chimera (or making sure you have the right version);
  2. Installing the DBPuppet extension;
  3. Configuring your browser to recognize files with the .chimerax suffix.

Installing Chimera

The DBPuppet extension will only work with versions of Chimera starting with build 1700. You can determine the version of your installed Chimera by choosing Version Info from the Help menu in Chimera. If this says UCSF Chimera, official version 1 build 1700 2003/03/26, then you can proceed to the next section, Installing the DBPuppet Extension. If your version of Chimera doesn't have a Version Info option under the Help menu, but instead has an item called About UCSF Chimera, then you probably have the newest build, 1864. If you do not have a recent enough version of Chimera (1700 or greater), you can get it from the Chimera Home Page. From this page, click on the Licensing and Download link in the top Quick Links section. Determine the appropriate file for your system. Each system type has an associated Instructions link that contains detailed instructions on how to install Chimera on your system. Before continuing on to the next section, Chimera must have completed its installation.

Installing the DBPuppet Extension

Unix

Download file DBPuppet.tar.gz from ftp://salilab.org/chimera . Save it to a temporary directory, such as /usr/tmp. Decompress is using the following command

% tar -xvzf /usr/tmp/DBPuppet.tar.gz

Then move the unzipped directory, named DBPuppet to the CHIMERA_ROOT/share/ directory, where CHIMERA_ROOT is the installation location of Chimera on your system. On Unix systems, the default is /usr/local/chimera:

% mv /usr/tmp/DBPuppet /usr/local/chimera/share/

Windows

Download the DBPuppet.zip file from ftp://salilab.org/chimera . Unzip it into a folder named DBPuppet. Move this folder to the CHIMERA_ROOT/share/ directory, where CHIMERA_ROOT is the installation location of Chimera on your system. On Windows systems, Chimera installs by default to C:\Program Files\Chimera

Configuring Your Browser

There are several ways to set up your system so that your web browser will properly handle files with a .chimerax suffix.

The easiest way to do this is to use the Browser Configuration utility that comes with the DBPuppet package. Look under Chimera's Tools menu for the DBPuppet group. The Browser Configuration tool will guide you through a series of dialogs that will help you set up your system's web browsers to recognize files with a .chimerax suffix.

If this is successful, you can skip the rest of these installation instructions and go to the section entitled Using the DBPuppet Extension.

If the Browser Configuration Tool does not work on your system, there are other ways to manually configure your browser:

Manual Configuration

Using the DBPuppet Extension

Actually using the DBPuppet extension is the easy part. In Chimera, click on Tools -> DBPuppet -> Database Control On. You will get a pop-up window saying Chimera is now listening for requests...

Once this has been enabled, clicking on the Chimera link from any ModBase entry will automatically open up the sequence alignment, and both the template and modeled structure in Chimera. If Chimera is not opened when the link is clicked, it will be automatically started, and the files will be opened. At this point, Chimera will be ready to accept subsequent requests from your web browser.

It is possible to set up Chimera so that it will automatically listen to browser requests upon startup. In order to do this, you need to enable Auto-start for the DBPuppet Control On tool as described here.