Focus supports a lot of image processing tasks in cryo-EM. To carry out many of these tasks, we depend on the great free software developed by the community. Some of these are essential for the functioning of Focus and others are optional. The required packages also depend on the technique you use for reconstruction. Here we list all the packages categorised as required and optional.

The softwares in this category are compulsory and MUST be installed independent of anything.

CSH is a Unix shell and a scripting language widely used in the electron microscopy field for historical reasons. One would not be able to run anything from FOCUS without CSH. It is already present on most systems, if not please install its improved successor, TCSH >6.0.

Many utilities and specific-purpose tools used by FOCUS are written in the Python scripting language (version 2.7.x). We recommend using a scientific Python installation like Anaconda or Canopy. You can also use the EMAN2.2 Python environment based on Anaconda (see below).

You also need pip and the module pil (or pillow).

On OSX, try

• xcode-select –install
• brew install deadline sqlite gdbm
• brew install python –universal –framework
• brew install libpng jpeg freetype
• sudo easy_install pip
• or try: sudo easy_install-3.6 pip
• easy_install pip
• pip install pillow

gawk is a more powerful version of the command-line utility awk. Install gawk on OSX with “brew install gawk”. On Linux, try “sudo apt-get install gawk”.

Many of the Python scripts called within FOCUS rely on the Python-MRCZ package. You can install mrcz in your Python environment with the following pip command:

pip install mrcz

EMAN2 is a great package with lots of tools available. We might not use the tools present in EMAN2 directly, but we definitely use python distribution attached with the source. EMAN2 is easy to install and is available for MacOS and Linux on their website: http://blake.bcm.edu/emanwiki/EMAN2

We directly use many command line utilities present in IMOD. It can be downloaded from the website: http://bio3d.colorado.edu/imod/

Focus uses CCP4 in order to generate merged maps of the protein in 2D crystallography projects. The software can be downloaded from http://www.ccp4.ac.uk/download.php. Please follow their installation guide.

Drift correction can be done using MotionCor2, Unblur or Zorro. In case you require to do the drift correction using one of these software, please install the required software using the links below:

• MotionCor2: http://msg.ucsf.edu/em/software/motioncor2.html
• Unblur: http://grigoriefflab.janelia.org/unblur
• Zorro: https://github.com/C-CINA/zorro

In all projects, CTF can be determined for each frame using CTFFIND4 or for the averaged frame using gCTF. These softwares need to be installed separately from the links below, if you wish to use them.

• CTFFIND4: http://grigoriefflab.janelia.org/ctffind4
• GCTF: http://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/

For 2D crystallography projects, CTF determination and correction is done using the CTFFIND3. The source code and executables are attached with the packages and you do not need to install it separately.

There are several other software packages listed below that are to be installed for specific purposes.

Particle picking can be done using following software:

• gautomatch: http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch/

If you wish to do SPR for 2D crystallography, you would need following dependencies.

• FREALIGN: http://grigoriefflab.janelia.org/frealign

For a hastle-free data transfer for remote monitoring, you would need to install following software:

• cadaver: Available with all the package managers