tymera_1.0

Custom Scripts

Installation

in order for the Python2.7 shell to import modules in this plugin, you must add the path to it.

In the Chimera GUI, go to Tools > Additional Tools > Add third-party plugin location... which should open up a dialog where you can click the [Add...] button and find the folder ONE LEVEL ABOVE tymera_1.0/. Clicking [Save] will add the path to the sys.path variable of of the Python2.7 shell.

Chimera will look for a ChimeraExtension.py file that defines a class for the plugin.

Class attributes include the submenu under which it will be located (e.g. Tools > '' > '') the name of the plugin that will be displayed '' and the action that is performed when you click on it In this case, the action is defined in tymera.py, which defines a function tymera_init() that simply imports all of the relevant packages in the plugin directory.

Each package directory (e.g., ColorBySeq) should have its own init.py to be recognized as something importable. For ColorBySeq and some others, the init.py also has instructions to import modules within that package.

For example, I believe color_by_seq() can be run in the IDLE with colorbyseq.color_by_seq() after activating tymera, since the colorbyseq.py module got imported.

in Python 2.7.14 Shell, enter the following reset the default path where scripts are opened to tymera/ if running on Windows:

import tymera os.chdir(os.path.dirname(tymera.file))

Demo Session

cd <tymera> chimera --script demo_8DD0.py