---
title: PDB Search inputs and parameters
description: >-
  Input formats, parameters, and validation for PDB structure search and
  download.
tags:
  - pdb
  - inputs
---

You provide either a free-text query to [search](/docs/pdb) 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).

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