The ISOLDE GUI

• What is ISOLDE all about?
• System Requirements
  • Operating System
  • Hardware
• GUI Details
  • Getting Started
    • Starting ISOLDE
    • Preparing a model for simulation
    • Adding maps
  • Visualisation and Navigation
    • General layout
    • Zooming and Panning
    • Adjusting the maps
    • Selecting atoms
    • Navigating and Masking
  • Basic simulation controls
    • Starting a simulation
    • Dealing with severe clashes
    • Dealing with unrecognised residues
    • General simulation controls
    • Basic interaction
    • Adjusting map weightings
    • Adjusting temperature and trajectory smoothing
  • Manipulating your model
    • Overview
    • Peptide flip and rotamer adjustment buttons
    • The Restraints tab
  • Monitoring the quality of your model
    • Peptide Bond Validation
    • The Ramachandran plot
    • Rotamer Validation
    • Clashes
    • Unparameterised Residues
  • Identifying problem “hotspots”
    • Overview
  • The ISOLDE menu
    • Model Building
    • Prep
• Tutorials
  • Introductory
    • Introduction to crystallographic model rebuilding in ISOLDE
    • Introduction to cryo-EM model rebuilding in ISOLDE
    • Dealing with severe clashes
  • Intermediate to Advanced
    • Top-Down Modelling with AlphaFold-DB Models
    • Improving Legacy Models Using AlphaFold
    • Building Into CryoEM Maps With Your Own AlphaFold Multimer Models
    • Starting From a Molecular Replacement Solution for a Flexible Protein
  • Superseded
    • Bulk Flexible Fitting