1. Install Phenix

See the installation notes for Phenix

2. Install gromacs_cryo_fit

Download gromacs-4.5.5_cryo_fit.zip at https://github.com/cryoFIT/cryo_fit_install

Install using a provided script.

% python <use phenix>/modules/cryo_fit/steps/0_install_cryo_fit/install_cryo_fit.py <cryo_fit.zip>

For example,

% python /Users/doonam/bin/phenix-dev-2906/modules/cryo_fit/steps/0_install_cryo_fit/install_cryo_fit.py ~/Downloads/gromacs-4.5.5_cryo_fit.zip

3. Troubleshooting

“-bash: libtbx.configure: command not found”

% Please run

% export PATH="/Users/doonam/bin/phenix-1.13rc1-2961/build/bin":$PATH

% source /Users/doonam/bin/phenix-1.13rc1-2961/phenix_env.sh

% in your commandline (of course, please change specific user path to your own phenix).

% and try “libtbx.configure cryo_fit” again

“subprocess.CalledProcessError: Command '['which', 'phenix.cryo_fit’]’”

% Literally, it can’t find phenix.cryo_fit

% Please link (sync) cryo_fit first by “libtbx.configure cryo_fit”. % If you have followed the installation protocol, simply open a new tab in your terminal (like iterm2), then your .bash_profile should run freshly.