Input formats, parameters, and validation for PDB structure search and download.

You provide either a free-text query to search the database or a 4-character PDB ID to download a specific structure — the orchestrator picks which from your phrasing. When a search returns several candidates, resolution is the input that most affects downstream quality: it is the primary criterion for choosing which structure to download.

Input methods

PDB has two operations on the platform: a search of the structure database and a download of a specific structure. Both run when you ask Ivy in chat; there is no form, job, or command for them.

Chat input (natural language)

Type a structure request in plain English. The orchestrator determines whether to search or download.

Search examples:

Search PDB for EGFR kinase structures
Find cryo-EM structures of the SARS-CoV-2 spike protein
Show me BRAF kinase structures with resolution below 2.0 Angstroms

Download examples:

Download 1M17 from PDB
Get the crystal structure 7JXO
Fetch PDB structure 3POZ in CIF format

What you can ask for

PDB search

You can set	Default	Limits
Query	Required	Protein name, organism, technique, ligand, or any keyword
Number of results	25	1-100

The search performs a full-text query against all PDB metadata fields including title, organism, experimental method, authors, and deposited ligand names.

PDB download

You can set	Default	Limits
PDB ID	Required	A 4-character PDB identifier (e.g., 1M17, 7BQY)
File format	PDB	PDB or mmCIF

Search query strategies

Protein name search

Search by protein name, gene name, or common names:

Search PDB for EGFR kinase domain, 10 results

Organism-specific search

Include the organism name in your query:

Search PDB for human insulin receptor, 15 results

Method-specific search

Filter by experimental method:

Search PDB for SARS-CoV-2 spike cryo-EM, 20 results

Ligand-based search

Find structures with specific bound ligands:

Search PDB for EGFR gefitinib, 10 results

Author search

Find structures deposited by specific researchers:

Search PDB for Yun CH EGFR, 25 results

PDB ID format

PDB identifiers follow a strict format:

Length: Exactly 4 characters
Pattern: Starts with a digit (0-9), followed by 3 alphanumeric characters
Examples: 1M17, 7BQY, 3POZ, 8DFN
Case: Case-insensitive (1m17 and 1M17 are equivalent; the platform converts to uppercase)

Extended PDB IDs

The PDB is transitioning to extended identifiers (PDB-Dev format) for future entries. Currently, all active entries use the 4-character format.

File format options

PDB format (default)

Extension: .pdb
Description: Legacy text-based format, widely supported by molecular viewers and analysis tools
Best for: DiffDock input, quick visualization, legacy tool compatibility
Limitations: Cannot represent very large structures (>99,999 atoms), limited precision for coordinates

mmCIF format

Extension: .cif
Description: Macromolecular Crystallographic Information File, the modern replacement for PDB format
Best for: Large structures, multi-model entries, complete metadata, new depositions
Advantages: No atom count limits, richer metadata, mandatory for new PDB depositions

Input validation

Search query validation

Minimum: Query must be a non-empty string
Special characters: Most characters are passed through to the RCSB Search API
Empty queries: Rejected with an error message

PDB ID validation

Format: Must match the pattern: one digit followed by three alphanumeric characters
Regex pattern: ^[0-9][A-Za-z0-9]{3}$
Invalid IDs: Return an error. Common mistakes include using UniProt accessions (6 characters) instead of PDB IDs (4 characters).
Non-existent IDs: Valid format but no structure exists. Returns a download error.

Limit validation

Minimum: 1
Maximum: 100
Default: 25
Values outside range: Clamped to nearest boundary

Example prompts

Search for high-resolution kinase structures

Search PDB for BRAF kinase high resolution, 10 results

Download a specific structure in PDB format

Download 1M17 from PDB in PDB format

Download a structure in mmCIF format

Download 7BQY from PDB in mmCIF format

Search for structures with bound drugs

Search PDB for EGFR erlotinib co-crystal, 15 results

Resolution guidelines for structure selection

When search results return multiple structures, resolution is the primary quality criterion for selecting which structure to download:

Resolution	Recommendation
<1.5 A	Excellent. Atomic-level detail, ideal for any analysis.
1.5-2.0 A	Very good. Suitable for docking, binding site analysis, and detailed modeling.
2.0-2.5 A	Good. Adequate for most structure-based drug design work.
2.5-3.0 A	Moderate. Backbone reliable, but side chain positions may be uncertain.
3.0-3.5 A	Low. Useful for overall fold and domain organization. Caution for detailed work.
>3.5 A	Very low. Limited to general topology. Not recommended for docking or binding analysis.

NMR structures do not have a resolution metric. Their quality is assessed by other metrics (ensemble RMSD, Ramachandran statistics).

PDB Search inputs and parameters