Configuring your local computer

Before you can use SAT, you will need to create a JSON EMDB-SFF file without geometrical annotations. The resulting file is very small and is easy to work with online, taking very little memory. To do this, you will configure your local computer by installing Python (if it is not present), creating a virtual environment then installing sfftk, the CLI tool to work with EMDB-SFF files.

Installing Python

Visit www.python.org and follow the instructions for your operating system. Note: Python may already be installed so first verify whether you need to install it.

Creating a virtual environment

It is highly recommended that you create a virtual environment when working on individual projects. This ensures complete separation of the Python associated with your project and that installed on your system. The two main options are:

• Virtualenv: This is the simplest option. Follow these instructions to create your virtual environment then activate it using these instructions.

• Conda: This is a bit more involved therefore only proceed if you have the experience and/or patience. Visit the Anaconda website to download and install it and for instructions on how to create and manage virtual environments.

Installing sfftk

In the virtual environment you created above run the following command:

pip install sfftk

Testing your installation

Once the installation is complete, test sfftk by running the following to view the list of available commands:

sff
usage: sff [-h] [-V] EMDB-SFF Read/Write Tools ...

The EMDB-SFF Toolkit (sfftk)

optional arguments:
  -h, --help                show this help message and exit
  -V, --version             show the sfftk-rw version string and the supported EMDB-SFF Read/Write version string

Tools:
  The EMDB-SFF Read/Write Toolkit (sff) provides the following tools:

  EMDB-SFF Read/Write Tools
    convert                 converts between EMDB-SFF formats
    view                    view file summary
    tests                   run unit tests
    prep                    prepares a segmentation
    config                  manage sfftk configs
    notes                   annotate an EMDB-SFF file

which should print out the list of available commands.