Tutorials

These tutorials are designed to provide you with step-by-step instructions, tips, and best practices for working with the ProLint2 tool, from setting up your initial environment to mastering advanced features.

• Tutorial #1: Working with the prolint2 Universe
  • Prerequisites
  • Creating a prolint2 Universe Instance
  • Accessing the Query and Database AtomGroups
  • Modifying the Query and Database AtomGroups
  • Computing Contacts
• Tutorial #2: prolint2 Universe Properties
  • Prerequisites
  • Displaying Current Universe Properties
  • Computing Contacts with Default Parameters
  • Changing Universe Parameters and Re-computing Contacts
  • Re-compute Contacts with Modified Parameters
• Tutorial #3: Introduction to the Contacts and Metrics objects
  • Prerequisites
  • Contact Output
  • Computing Contact Metrics
  • Output Formats
  • Creating and Adding Metrics to the Registry
  • Converting Output Formats
  • Convenience Function: create_metric
• Tutorial #4: Residence Time Calculations
  • Prerequisites
  • Understanding Residence Time Calculations
  • Setting Up Parameters
  • Computing Residence Time
• Tutorial #5: Building Complex Contact Schemas
  • Prerequisites
  • Overview of Complex Contact Schemas
  • Compute Contacts at Different Cutoffs
  • Using Double Cutoffs
  • Understanding the Logic
  • Constructing More Complex Schemas
  • Annular Shell Contacts