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/
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
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:
Description of type: Chimera Puppet File File extension: chimerax MIME type: application/x-chimerax Application to use: CHIMERA_ROOT/share/DBPuppet/send_to_chimeraSubstitute the installation location of Chimera on your system for
CHIMERA_ROOT
.
The default installation of Chimera is /usr/local/chimera
Check for the following files in your home directory:
HOME_DIR/.mime.types
Unix systems use this file to identify different types of files downloaded from the web. If this file does not exist, create it and add the following line:
application/x-chimerax chimerax
HOME_DIR/.mailcap
Unix systems use this file to associate file types with applications.
If this file does not exist, create it and add the following line:
application/x-chimerax CHIMERA_ROOT/share/DBPuppet/send_to_chimera %s
where CHIMERA_ROOT
is the path to the top level of your Chimera installation.
For example, if Chimera was installed in /usr/local/chimera
(the default), the line in your .mailcap
file would look like:
application/x-chimerax /usr/local/chimera/share/DBPuppet/send_to_chimera %s
If this file does exist, add the above at the end of the file on a new line
Action: open
Application used to perform action:
C:\PYTHON_ROOT\pythonw.exe "C:\CHIMERA_ROOT\share\DBPuppet\send_to_chimera.py" "%1"
Be sure to include the quotes.
Substitute the location of the Python that Chimera installed for PYTHON_ROOT
(default is C:\Python22
) and the
installation location of Chimera for CHIMERA_ROOT
(default is C:\Program Files\Chimera
) .
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.