---
title: AlphaFold troubleshooting
description: Recover from a structure-not-found miss, a case-sensitive UniProt ID, EBI outages, red low-pLDDT regions, and a result that is one chain with no ligands.
---

When [AlphaFold Fetch](/docs/alphafold) fails or returns something unexpected, this page covers the common failure modes — from "structure not found" and invalid UniProt IDs to low-confidence regions, EBI availability errors, and the monomer-without-ligands nature of the result.

## Troubleshooting

## "Structure not found in AlphaFold Database"

The most common failure mode. The protein you asked for is not in the database.

**Common causes:**
- The UniProt entry is from an organism not covered by the AlphaFold DB campaign
- The accession is unreviewed (TrEMBL) and was not included in the bulk run
- The entry is a fragment, peptide, or non-standard record

**Recovery:**

1. **Easiest** — switch to ESMFold: *"Predict the structure with ESMFold using the UniProt sequence"*. The platform will fetch the sequence and run [ESMFold](/docs/esmfold).
2. **Fallback in one request** — ask *"Try AlphaFold first; if it is not in the database, run ESMFold."* The [orchestrator](/docs/how-orchestration-works) chains both steps.
3. **Manual check** — visit `https://alphafold.ebi.ac.uk/entry/{uniprot_id}` to confirm the gap before re-running.

## "Invalid UniProt ID"

The accession failed validation.

**Common causes:**
- Typo (UniProt accessions are case-sensitive — `p00533` is invalid, `P00533` is valid)
- You passed a gene symbol (`EGFR`) instead of an accession (`P00533`)
- You passed a PDB ID (`6LU7`) instead of a UniProt accession

**Recovery:** ask in chat *"Find the UniProt accession for <name>"* and re-run with the result.

## Structure loaded but quality looks poor

The structure fetched fine, but large regions are red/orange in the 3D viewer (pLDDT < 70).

**This is usually correct.** AlphaFold legitimately reports low confidence for:

- **Intrinsically disordered regions** — flexible loops, signal peptides, transactivation domains
- **Termini** — N- and C-terminal regions often score below 50
- **Linkers** — flexible regions connecting structured domains

If the low-confidence regions matter for your downstream analysis (e.g. docking, binding-site work), focus on the high-confidence core domains and treat low-confidence regions as unreliable.

## Network / availability errors

The fetch calls the EBI public endpoint at `https://alphafold.ebi.ac.uk`. If EBI is down or slow:

- Retry after 30–60 seconds — transient failures are common for any public API
- If persistent, switch to [ESMFold](/docs/esmfold) — it runs on the platform's own GPUs and does not depend on EBI

## Multiple AlphaFold versions

The AlphaFold DB has shipped several model versions, and its prediction API reports both the current one (`latestVersion`) and the full list (`allVersions`). The fetch returns the **`F1`** entry for the accession at whatever version the API currently names — it does not hardcode one, because EBI deletes the old file keys on a version bump and a stale version 404s for every accession.

So the version you get can change between runs. Record `modelVersion` from the result alongside any figure you derive from the structure.

If you need a specific older version for reproducibility against a published paper, that's not something you can ask for: the fetch always takes the version the API currently names. Download that version manually from EBI.

## Downstream tool says "PDB has no ligands / no chain B"

AlphaFold predictions are **monomers without ligands**. The PDB file has:

- A single chain (A)
- No bound ligands, ions, or cofactors
- No crystal-packing artifacts

For docking, this is what you want. For complex-aware analysis (e.g. studying a protein's native cofactor environment), ask for the [PDB entry](/docs/pdb) instead — experimental structures usually include ligands.

## Read next