19  Appendix: PyMol for BSF

Install Pixi

  1. Click the clipboard icon at the right end of the box below to copy the command to your clipboard.
  2. Open your Terminal application.
  3. Paste the command into the Terminal window and press Enter. You will be prompted several times for either your user password or permissions of the installed apps.
curl -fsSL https://pixi.sh/install.sh | sh
  1. Click the clipboard icon at the right end of the box below to copy the command to your clipboard.
  2. Open your PowerShell application.
  3. Paste the command into the PowerShell window and press Enter. You will be prompted several times to allow the app to make changes to your computer.
powershell -ExecutionPolicy ByPass -c "irm -useb https://pixi.sh/install.ps1 | iex"

If that fails, you can download this interactive installer and run it.

Install PyMol

  1. Create a folder on your computer dedicated to the BSF course. Let’s say you call it ‘BSF’ and put it in your ‘Documents’ folder.
  2. Open your Terminal application, and navigate to that folder using cd (something like cd Documents and then cd BSF).
  3. Once you are in the ‘BSF’ folder, paste the command into the Terminal window and press Enter. You will be prompted several times for either your user password or permissions of the installed apps.
pixi init --platform osx-64 -c conda-forge -c anaconda -c schrodinger && pixi config set --local run-post-link-scripts insecure && pixi add pyqt "pymol-bundle=3.1" "vtk-m=1.8"
  1. Create a folder on your computer dedicated to the BSF course. Let’s say you call it ‘BSF’ and put it in your ‘Documents’ folder.
  2. Open your PowerShell application, and navigate to that folder using cd (something like cd Documents and then cd BSF).
  3. Once you are in the ‘BSF’ folder, paste the command into the PowerShell window and press Enter. You will be prompted several times to allow the app to make changes to your computer.
pixi init -c conda-forge -c anaconda -c schrodinger ; pixi config set --local run-post-link-scripts insecure ; pixi add pyqt "pymol-bundle=3.1" "vtk-m=1.8"

Running PyMol

In your BSF folder, run:

pixi run pymol