RCSB Protein Data Bank skill

Prerequisites

uv
: Read the
```
uv
```
skill and follow its Setup instructions to ensure
```
uv
```
is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://www.rcsb.org/pages/usage-policy, then (2) create the file recording the notification text and timestamp.

Core Rules

Always prefer to use the provided scripts. Only as a last resort use
```
curl
```
,
```
urllib
```
, raw HTTP requests, or any other method to access PDB APIs. The scripts automatically enforce required rate limits.
Always redirect output to a file. Parse output with e.g.
```
jq
```
,
```
grep
```
, or a short Python snippet. Do NOT print large API responses to stdout to avoid truncation.
Notification: If this skill is used, ensure this is mentioned in the output.
Explain your queries On completing a task that used PDB JSON/GraphQL queries, explain in clear language what your query did so the user can correct any bad assumptions.

Attribute-based search workflow

Fetch the relevant schema to discover searchable attribute names. For structure attributes:

uv run scripts/fetch_schema.py --api search_structure --output schema_structure.txt

For chemical attributes:

uv run scripts/fetch_schema.py --api search_chemical --output schema_chemical.txt

Grep the schema to find relevant attributes. Grep one keyword at a time and examine many lines — there are lots of similar attributes and you must choose the best match for the user's intent.
Compose and run a JSON search query using the discovered attributes:
```
uv run scripts/search_pdb.py --query '<JSON>' --return_type <RETURN_TYPE> --output results.json
```
Pass the
```
--count_only
```
flag to get just the number of matching entries.

For step 2: some basic PDB concepts (helpful for attribute choice)

Entity: A unique molecule found in a structure.
Instance / Chain: A particular copy of an entity. E.g. if a structure contains two protein chains with the same sequence, they are the same entity but different instances / chains.
Assembly: A biologically relevant collection of instances / chains. This may be the same as the deposited structure, a subset, or multiple copies.
Label vs Auth: Polymer instances get letter labels ("A", "B", "AA") and their monomers are numbered. There are author-assigned ("auth") and PDB-internal ("label") schemes. The label scheme is more consistent and is always used in scripts and APIs. However, users and papers may refer to the author scheme (clarify which scheme is being used if necessary).
Chemical component: A small molecule / monomer, with an ID matching
```
[A-Z]{1,3}
```
Primary citation: The main publication about a structure. Prefer
```
primary_citation
```
attributes over
```
citation
```
attributes.
Resolution: Frequently used measure of structure quality (lower is better). Usually prefer
```
rcsb_entry_info.resolution_combined
```
, which accounts for different experimental methods.

For step 3: Example queries

bash

# Non-human proteins published in Nature, newest first
uv run scripts/search_pdb.py --query '{ "type": "group", "logical_operator": "and", "nodes": [ { "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "negation": true, "value": "Homo sapiens", "attribute": "rcsb_entity_source_organism.taxonomy_lineage.name" } }, { "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "value": "Nature", "attribute": "rcsb_primary_citation.rcsb_journal_abbrev" } } ] }' --return_type entry --sort_by rcsb_accession_info.initial_release_date --sort_direction desc --page_start 0 --rows 100 --output results.json

bash

# Structures containing the chemical component CA (Ca2+ ion)
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "text_chem", "parameters": { "operator": "exact_match", "value": "CA", "attribute": "rcsb_chem_comp_container_identifiers.comp_id" } }' --return_type entry --output results.json

bash

# Number of entries with disulfide bonds
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "value": "disulfide bridge", "attribute": "rcsb_polymer_struct_conn.connect_type" } }' --return_type entry --count-only --output count.json

Common operators:

exact_match

equals

exists

contains_phrase

contains_words

in

greater

less

Similarity-based search workflow

Similarity searches do not require a schema fetch. Basic examples:

bash

# Sequence similarity
uv run scripts/search_pdb.py --query '{ "query": { "type": "terminal", "service": "sequence", "parameters": { "evalue_cutoff": 1, "identity_cutoff": 0.9, "sequence_type": "protein", "value": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ" } }, "request_options": { "scoring_strategy": "sequence" } }' --return_type polymer_entity --output results.json

bash

# Structure similarity
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "structure", "parameters": { "value": {"entry_id": "6LU7", "asym_id": "A"}, "number_of_candidates": 2000 } }' --return_type polymer_entity --output results.json

bash

# Sequence motif match
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "seqmotif", "parameters": { "value": "C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H.", "pattern_type": "prosite", "sequence_type": "protein" } }' --return_type polymer_entity --output results.json

bash

# Chemical descriptor match
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "chemical", "parameters": { "value": "InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11H,1H3,(H,9,10)", "type": "descriptor", "descriptor_type": "InChI", "match_type": "graph-strict" } }' --return_type mol_definition --output results.json

See https://search.rcsb.org/#search-services for more details.

Full text search workflow

Searches all text associated with an entry. Example:

bash

uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "full_text", "parameters": { "value": "isopeptide + ( collagen | fibrinogen )" } }' --return_type entry --output results.json

Important: use
full_text
search as a last resort when there's no more precise attribute search available. Consider using the
struct.title
or
rcsb_pubmed_abstract_text
attributes instead.

File download workflow

To download full PDB entries, use the

download_coordinate_files.py

script. Use this when you need access to atomic coordinates, when asked for a pdb / mmcif file, or when non-specifically asked to fetch a PDB code. Example:

bash

uv run scripts/download_coordinate_files.py --ids "4HHB,6BEA" --format "mmcif" --output_dir <OUTPUT_DIR>

Metadata query workflow

This flow is significantly more efficient than downloading full coordinate files when you only need a few pieces of metadata about each entry / entity.

Fetch the schema for the relevant object type. E.g.

uv run scripts/fetch_schema.py --api data_entry --output schema_entry.txt

Grep the schema for relevant fields (one keyword at a time, many lines).

Compose and run a GraphQL metadata query:

uv run scripts/fetch_pdb_metadata.py --query '<GraphQL>' --output results.json

For step 3: Example queries

bash

# Fetch structure titles and experimental methods
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids: ["1STP", "2JEF", "1CDG"]) { rcsb_id struct { title } exptl { method } } }' --output results.json

bash

# Fetch polymer entity taxonomy and cluster membership
uv run scripts/fetch_pdb_metadata.py --query '{ polymer_entities(entity_ids:["2CPK_1","3WHM_1","2D5Z_1"]) { rcsb_id rcsb_entity_source_organism { ncbi_taxonomy_id ncbi_scientific_name } rcsb_cluster_membership { cluster_id identity } } }' --output results.json

bash

# Fetch polymer entity external sequence database accessions
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids:["7NHM", "5L2G"]){ polymer_entities { rcsb_id rcsb_polymer_entity_container_identifiers { reference_sequence_identifiers { database_accession database_name } } } } }' --output results.json

pdb-database

NPX Install

Tags

SKILL.md Content

RCSB Protein Data Bank skill

Prerequisites

Core Rules

Attribute-based search workflow

For step 2: some basic PDB concepts (helpful for attribute choice)

For step 3: Example queries

Similarity-based search workflow

Full text search workflow

File download workflow

Metadata query workflow

For step 3: Example queries