Load Structure

Instructions for uploading and processing structural models in SAXS-A-FOLD.

Overview

The "Load Structure" tab allows users to upload structural models or retrieve them from databases like AlphaFold. These models are used for advanced calculations, including the determination of physical and structural parameters.

Steps to Load a Structure

  1. Access the Load Structure Tab: Navigate to the Load Structure tab from the main interface.
  2. Select Input Source: Click on the Select input source field to choose one of the following:
    • Input PDB or CIF:
      • Browse local files: Upload a file from your computer.
      • Browse server: Retrieve previously uploaded files from the server.
    • Get AlphaFold structure:
      • Accesses the AF2 database (https://alphafold.ebi.ac.uk).
      • Enter a UniProt accession code in the provided field. Typing part of it and pressing Process will list up to 25 matching AF2 entries.
      • Choose the desired structure from the list of matches.
    • Get Post Translationally Modified AFv2 structure:
      • Accesses the US-SOMO AFv2 database database (https://somo.genapp.rocks/somoaf).
      • Enter a UniProt accession code in the provided field. Typing part of it and pressing Process will list up to 25 matching US-SOMO AFv2 entries.
      • Choose the desired structure from the list of matches.
  3. Set Solvent Electron Density: Adjust the Solvent electron density [e/ų] field if necessary (default: 0.335). This value is used in I(q) calculations performed on structures.
  4. Process the Structure: Click Process to perform a series of calculations on the uploaded or retrieved model structure. The calculations include:
    • Physico-chemical and structural parameters using a local installation of the US-SOMO program.
    • P(r) and I(q) calculations, with the latter performed using a WAXSiS (https://waxsis.uni-saarland.de) local installation.
    A progress bar and associated messages will indicate the status of the calculations.

Outputs and Visualization

Once the structure is processed:

  • The Name field shows a composite of the original file name and an extension related to the program used to generate the listed parameters.
  • The Title and Source fields are populated if the entry comes from the AlphaFold database; otherwise, they depend on the uploaded PDB structure's content.
  • The Warnings field will indicate any issues encountered during processing, or display No warnings if none are present.
  • A dry structure P(r) plot is shown, scaled to the experimental counterpart.
  • WAXSiS I(q) calculations are displayed, scaled to the experimental I(q) data.

In the P(r) plot, frequencies are normalized by the structure's calculated molecular mass. For the I(q) plot, error-weighted residuals between experimental and calculated curves are shown, while the P(r) plot does not use error weighting.

Below the plots, the RMSD of the scaling and the normalized χ² ("nChi²") for I(q) are reported.

Full Listing of Outputs

At the bottom of the tab, a detailed listing of US-SOMO processing output is provided, including:

  • Identified disulfide bridges.
  • Amino acid sequence in three- and one-letter codes.
  • Overall amino acid composition and various physico-chemical parameters.
  • A log of the operations involved, including those related to WAXSiS processing.

Users can assess the agreement between experimental and calculated data from the I(q) and P(r) comparisons. If significant differences exist, further actions may be required to achieve better fit, such as refining the model.

Finalizing the Process

Pressing Submit will add the structure and all calculated parameters to the project. On returning to the project, this tab does not need to be accessed again.

Return to Main Help