EMBL ATSASfold

User guide

ATSASfold help

A short guide to starting a project, following an analysis, and refining structure if needed.

Quick start

  1. 1 Create a project. Sign in, open your dashboard, and give the project a recognizable title.
  2. 2 Upload SAXS data. Add the experimental .dat file (check box if data is in A^-1).
  3. 3 Add the sequence and structure. Paste or upload a sequence, then provide an AlphaFold model as a .zip file, or separate files.
  4. 4 Review the summary and recommendation. Inspect the plots, given values and warnings before accepting a category or starting follow-up analysis.
  5. 5 Determine domains. Using the 3D viewer and interface, determine rigid domains and flexible linkers. Use automated segmentation as a guide
  6. 6 ATSAS online. Submit a project to ATSAS online and wait until the calculations are finished.
  7. 7 Results. Analyse and download results of different runs.
Sign in to begin

Input files

SAXS data

Upload a text .dat file containing numeric SAXS data. It should contain three columns - q, I(q), σ(q). Check that the displayed curve and q range look reasonable before running the primary analysis.

Protein sequence

Paste a sequence or upload a .fasta, .fa, .seq, or .txt file. Confirm that it is the same construct used for the SAXS measurement, including any tags or missing residues that affect molecular weight.

Structure and AlphaFold files

Structure uploads can use PDB, CIF, or mmCIF. ATSASfold also accepts related AlphaFold confidence data or a .zip archive where offered by the upload form. If you run inference with the other model and the data is not processed, please let us know.

Analysis workflow

Primary analysis
ATSASfold inspects the raw SAXS curve and next, via ATSAS tools, estimates quantities such as the usable q range and protein size. Some warnings may be generated, notifying about possible data/analysis problems.
Sequence and molecular weight
The sequence-derived molecular weight is compared with SAXS estimates. A serious mismatch may indicate a different oligomeric state, concentration issue, or problematic data and is reported.
AlphaFold fit and classification
CRYSOL is used to compare the supplied atomic structure with the SAXS experimental curve. ATSASfold combines fit and data features to suggest an analysis category and possible next step.
Follow-up analysis
Depending on the result and available inputs, the project can prepare or submit an appropriate ATSAS Online workflow and later display downloaded results.

Defining domains

For domain-based or flexible modelling, divide the structure into regions that should move as rigid bodies and residues that can act as flexible linkers. Open Domains & ATSAS from the project summary when this follow-up is available.

Start from a proposal

Use the Chainsaw suggestion or generate boundaries with af_segmentation for a chosen number of domains. You can use these automated proposals are starting points.

Review the structural evidence

Inspect the proposed regions in the 3D view and against the pLDDT and PAE plots. Domain coloring separates rigid regions, while flexible residues are shown in grey.

Adjust and save the regions

Split, delete, or edit rigid domains as needed; uncovered residues are treated as flexible, and rigid ranges must not overlap. Review any warning about the number of fitted parameters, then select Save domains before submitting to ATSAS online.

ML classification

The classificator category is a recommendation, based on an XGBoost classifier trained on SASBDB dataset. This means, that the selected class is heavily affected by the depositor-reported choices.

Fixed

The supplied structure appears consistent with the measured SAXS data.

Rigid

A rigid-body or domain-based modelling may improve the SAXS fit.

SREFLEX

Normal-mode refinement may improve the agreement between the structure and the SAXS curve.

EOM

An ensemble description may be appropriate for a flexible or heterogeneous system.

ATSAS Online

Your dashboard shows whether an ATSAS Online account is connected. Online submissions run in the background, so a queued or running state is normal. Wait for the notification email. If the connection status looks stale, use Recheck on the dashboard.

Troubleshooting

The uploaded curve looks wrong

Check that the file contains the intended dataset and numeric columns, then confirm the selected q units and range. Replace the upload if the wrong file was used.

The sequence and SAXS molecular weights disagree

Verify the construct sequence, tags, oligomeric state, sample concentration, and whether the SAXS estimate is reliable for this dataset. Keep in mind that the quality of SAXS-based Mw determination depends heavily on the SAXS data quality.

A job is still queued or running

Longer calculations and remote ATSAS Online jobs may take time. You can leave the page and revisit the project later. Report it if the state does not change after a reasonable wait.

A step failed

Read the message shown with the failed step and correct any missing or invalid input before retrying. Do not hesitate to contact us if failure persists. Please include the project name, failed step, and displayed message.

Still need help?

Sign in to send feedback from the application, or email atsasfold@embl-hamburg.de.