Structural Info / Flexible Regions

Instructions for exploring and defining flexible regions in SAXS-A-FOLD.

Overview

The Structural info / Flexible regions tab is used to analyze flexible regions in structural models. It allows users to auto-compute flexible regions from AlphaFold residue confidence values or manually define them.

This tab is the first that should be re-accessed after returning to a project. After selecting a project in the Define Project tab, this tab displays previously computed structural parameters along with the I(q) and P(r) plots from the earlier tab.

Steps to Analyze Flexible Regions

  1. View Structural Data: At the top of the webpage, structural parameters and the I(q) and P(r) plots from the previous tab are re-shown for reference.
  2. Explore the Structure: The structure is displayed again below the plots in a JSmol interactive representation.
  3. Auto Compute Flexible Regions:
    • Enable the Auto compute flexible regions from AlphaFold residue confidence switch (works only on AlphaFold-generated structures).
    • Enter a confidence threshold in the Confidence level for Auto compute field (default: 60). This threshold identifies sequences of at least five consecutive residues with confidence levels below the chosen value.
    • Press Compute flexible regions to analyze the structure. This generates additional fields corresponding to the number of flexible regions found, as indicated in the Number of flexible regions field (default: 1).
    • The identified flexible regions will be listed in the Flexible region start,end [#] field(s). These regions will be highlighted in green in the updated JSmol plot.
  4. Manually Define Flexible Regions (Optional):
    • If the auto-compute results are unsatisfactory, turn off the auto-compute switch.
    • Manually populate the Number of flexible regions and Flexible region start,end [#] fields. For example, to define one flexible region, enter the start and end residue numbers (e.g., 170, 210).
  5. Submit Flexible Regions: Press Submit to store the final choice for the flexible regions parameters.

Tips for Exploration

Users can experiment with different threshold values in the auto-compute routine to refine the flexible regions. Each modification updates the JSmol plot and provides immediate feedback on the impact of the chosen threshold.

Return to Main Help