easypipe’s documentation

You can also grab a hardcopy of the easYPipe documentation in PDF

• Getting started (Linux)
  • Check your python version
  • Check if pip is installed
  • Software requirements
    • Phenix
    • Open Babel
  • Download and install easypipe package
  • Check easypipe installation
  • Uninstall easypipe package
  • References
• Getting started (Windows)
  • Check your python version
  • Software requirements
    • Phenix
    • Open Babel
    • Advices
  • Download and install easypipe package
  • Check easypipe installation
  • Uninstall easypipe package
  • References
• easYGet
  • easYGet usage
  • What does it do ?
• easYPipe
  • easYPipe usage
    • References
• easYPipe quickstart guide
  • 1. Retrieve and organize your processed data
  • 2. Prepare the data with ‘prep’
  • 3. Reindex if necessary with ‘reindex’
  • 4. Add ligands with ‘ligands’
  • 5. Process the data with ‘launch’
    • Mode
    • Ligand search
    • Datasets to treat
  • 6. Compile results in a summary file
  • 7. Automatic mode
• easYPipe ‘prep’
  • Usage
  • How the data should be organized ?
  • What does it do ?
  • References
• easYPipe ‘reindex’
  • Usage
  • What does it do ?
  • Reindex simulation mode
  • References
• easYPipe ‘ligands’
  • Usage
  • What does it do ?
  • References
• easYPipe ‘launch’
  • Usage
  • What does it do ?
    • 1. Sort mtz files according to space group in reference pdb, and decreasing completeness
    • 2. List mtz files according to option ‘best’, ‘autoproc’ or ‘whole’
    • 3. List mtz files with mode and ligand information for running Phenix
    • 4. Launch Phenix according to chosen mode and options - Simulation mode
    • 5. Write results
  • Phenix options according to modes (only for information)
  • References
• easYPipe ‘summary’
  • Usage
  • What does it do ?
• easYPipe ‘auto’
  • Usage
  • How the data should be organized ?
  • What does it do ?
• easYPipe ‘pandda’
  • Usage
  • What does it do ?
  • References