1. Install Phenix

See the installation notes for Phenix

2. Link cryo_fit to phenix

At <user phenix>/modules

git clone git@github.com:cryoFIT/cryo_fit.git

At any folder,

libtbx.configure cryo_fit

3. Download cryo_fit install file

Download gromacs-4.5.5_cryo_fit.zip from here

4. Install cryo_fit

• If a user's OS is either macOS or linux, install using a provided script.

• python <user phenix>/modules/cryo_fit/files_for_steps/0_install_cryo_fit/install_cryo_fit.py <cryo_fit.zip> <install_path>

• If <install_path> doesn't exist when a user specifies it, a new folder with that name will be created (confirmed at macOS 10.13.6).
• Please use an absolute path. For example,

• python /Users/doonam/bin/phenix-dev-2906/modules/cryo_fit/files_for_steps/0_install_cryo_fit/install_cryo_fit.py ~/Downloads/gromacs-4.5.5_cryo_fit.zip ~/cryo_fit
• will work.

• However, a relative path like,

• python /Users/doonam/bin/phenix-dev-2906/modules/cryo_fit/files_for_steps/0_install_cryo_fit/install_cryo_fit.py ~/Downloads/gromacs-4.5.5_cryo_fit.zip ..
• doesn't work.

• If a user has windows OS, install_cryo_fit.py may not work.

• Doo Nam recommends either macOS or linux OS.
• If a user needs to use Windows OS, a user may analyze install_cryo_fit.py code, and run commandline commands by him/herself.
• Alternatively, a user may use cryo_fit2.

5. Troubleshooting

• If user's OS doesn't have git
  • install git
• If a user sees the error message during git clone, “Permission denied (publickey).fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists.”,
  • user’s computer needs to be registered to his/her github account. Therefore, make github account (free), Generate a new SSH key and Add a new SSH key to your GitHub account
• If user's macOS shows, “xcode-select: note: no developer tools were found at '/Applications/Xcode.app', requesting install. Choose an option in the dialog to download the command line developer tools.”
  • download commandline as instructed (this may take ~7 minutes)
• “-bash: libtbx.configure: command not found”
  • (in commandline)
  • export PATH="/Users/.../phenix-xxxx/build/bin":$PATH
  • source /Users/.../phenix-xxxx/phenix_env.sh
  • libtbx.configure cryo_fit

6. Test run

See the cryo_fit1 tutorial