User Guide

This section explains the basics of using MolCube-API Client, and shows some examples of common operations. For an in-depth description of the available modules, functions, classes, etc., see API Reference.

This guide contains links to the API Reference whenever an important function or data type is introduced. They look like this: PdbReaderProject.

Contents:

• PDB Reader
  • Background
  • Overview
  • Setup PDB Reader project
  • Check available info about PDB
  • Using default settings
  • Confirm chain selection (required)
  • Model manipulation (required)
  • Supported manipulations
  • Selecting different chains
  • Terminal patching
  • Mutations
  • Phosphorylation and protonation
  • Disulfide bonds
  • Peptide Stapling
  • Missing residues
  • Handling ligands and nonstandard residues
  • Side chain orientation
• Glycosylation
  • Check default GLYC Chains
  • Understanding Glycosylation Structure
  • Building a Glycosylation Structure
  • Managing Glycosylations in PDBReader
  • Common Errors and Constraints
• Solution Builder
  • Create Solution Builder project
• Membrane Builder
  • Create Membrane Builder Project
• Ligand Modeler
  • Create Ligand Modeler project
  • Modify SDF file (optional)
• Free Energy
  • Creating a Alchemical Free Energy Simulator Project
  • AMBER-TI Relative Binding