RCSB PDB Sequence Coordinates API changes

Migrating from the 1D Coordinates Service to the Sequence Coordinate Service involves updating your endpoint URLs to call the new service and modifying your applications to account for breaking changes introduced in the new API.

The RCSB PDB 1D Coordinates Service API will be deprecated on November 23, 2024. The final removal of this service will occur on May 31, 2025 at which point queries to https://1d-coordinates.rcsb.org/graphql will no longer work. Programmatic users must adapt queries to be compatible with the Sequence Coordinates Service available at https://sequence-coordinates.rcsb.org/graphql and use the new API in the requests URLs by May 31, 2025.

HTTP Request

The Sequence Coordinates Service API only support HTTP POST requests.

End Points

Endpoint alignment has been renamed to alignments.

1D Coordinates Service	Sequence Coordinates Service

Endpoint group_alignment has been renamed to group_alignments.

1D Coordinates Service	Sequence Coordinates Service

End Points Arguments

Endpoint group_annotations boolean argument histogram has been removed. Its functionality has been replaced by a new endpoint group_annotations_summary with the same signature.

1D Coordinates Service	Sequence Coordinates Service

Enumerated values of GroupReference are now screaming snake case

MATCHING_UNIPROT_ACCESSION
SEQUENCE_IDENTITY

1D Coordinates Service	Sequence Coordinates Service

Query Fields

Field target_alignment has been renamed to target_alignments.

1D Coordinates Service	Sequence Coordinates Service

Field target_alignment_subset has been removed. The motivation of this field was to request a subset of alignment based on offset and length arguments. This functionality has been moved to target_alignments field that accepts optional arguments as the removed field.

1D Coordinates Service	Sequence Coordinates Service

Type Names

GraphQL type name changes. This only affects programmatic users that build types from GraphQL schema

FilterInput type has been renamed to AnnotationFilterInput
Source type has been renamed to AnnotationReference
AlignmentResponse type has been renamed to SequenceAlignments
AnnotationFeatures type has been renamed to SequenceAnnotations
AdditionalProperties type has been renamed to FeaturesAdditionalProperties
Type type has been renamed to FeaturesType
FeaturePositions type has been renamed to FeaturesFeaturePositions
AlignedRegion type has been renamed to AlignedRegions
Feature type has been renamed to Features

Contact Us

Contact info@rcsb.org with questions or feedback about this service.