16. A Note on Software Installation

All the protocols shown in this document are available in the stable release 3.0.6 (code name Eugenius). This is a major release in which protocols are published as “plugins”. Required plugins for each protocol are indicated in respective Appendices. Follow the instructions to install each plugin (scipion-em).

In addition to the standard and scipion plugins installation, you need to install the following packages:

• CCP4 (v. 7.0.056 or higher; protocols have been tested with v. 7.1): Connect to CCP4 and follow instructions.

• Phenix: Connect to PHENIX and follow instructions. Protocols have been tested for versions 1.13-2998, 1.16-3549, 1.17.1-3660, 1.18.2-3874, 1.19.2-4158 and 1.20.1-4487.

• Clustal Omega: Run sudo apt-get install clustalo (in ubuntu).

• MUSCLE: Run sudo apt-get install muscle (in ubuntu).

Finally, (1) edit the file /.config/scipion/scipion.conf and set the right values for the variables CCP4_HOME and PHENIX_HOME, and (2) execute scipion config –update