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CoordinateServer API reference

Residues Inside a Sphere /ambientResidues

Identifies all residues within the given radius from the source residue.

Example

/1cbs/ambientResidues?authAsymId=A&authName=REA&authSeqNumber=200&radius=5

Parameters

Name Type Default Description
entityId String Corresponds to the '_entity.id' or '*.label_entity_id' field, depending on the context.
asymId String Corresponds to the '_atom_site.label_asym_id' field.
authAsymId String Corresponds to the '_atom_site.auth_asym_id' field.
name String Residue name. Corresponds to the '_atom_site.label_comp_id' field.
authName String Author residue name. Corresponds to the '_atom_site.auth_comp_id' field.
insCode String Corresponds to the '_atom_site.pdbx_PDB_ins_code' field.
seqNumber Integer Residue seq. number. Corresponds to the '_atom_site.label_seq_id' field.
authSeqNumber Integer Author residue seq. number. Corresponds to the '_atom_site.auth_seq_id' field.
radius Float 5 Value in Angstroms.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Assembly /assembly

Constructs assembly with the given id.

Example

/1e12/assembly?id=1

Parameters

Name Type Default Description
id String 1 Corresponds to the '_pdbx_struct_assembly.id' field.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _cell, _symmetry, _struct_conf, _struct_sheet_range, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Backbone Atoms /backbone

Atoms named N, CA, C, O, P, OP1, OP2, O3', O5', C3', C4, C5' from polymer entities.

Example

/1cbs/backbone

Parameters

Name Type Default Description
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Cartoon Representation /cartoon

Atoms necessary to construct cartoons representation of the molecule (atoms named CA, O, O5', C3', N3 from polymer entities) + HET atoms + water.

Example

/1cbs/cartoon

Parameters

Name Type Default Description
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Specific Chains /chains

Chains that satisfy the given parameters.

Example

/1cbs/chains?authAsymId=A

Parameters

Name Type Default Description
entityId String Corresponds to the '_entity.id' or '*.label_entity_id' field, depending on the context.
asymId String Corresponds to the '_atom_site.label_asym_id' field.
authAsymId String Corresponds to the '_atom_site.auth_asym_id' field.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Specific Entities /entities

Entities that satisfy the given parameters.

Example

/1cbs/entities?type=polymer

Parameters

Name Type Default Description
entityId String Corresponds to the '_entity.id' or '*.label_entity_id' field, depending on the context.
type String Corresponds to the '_entity.type' field (polymer / non-polymer / water).
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Full Structure /full

The full structure.

Example

/1cbs/full

Parameters

Name Type Default Description
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

HET Atoms /het

All non-water 'HETATM' records.

Example

/1cbs/het

Parameters

Name Type Default Description
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Ligand Interaction /ligandInteraction

Identifies symmetry mates and returns the specified atom set and all residues within the given radius.

Example

/1cbs/ligandInteraction?authAsymId=A&authName=REA&authSeqNumber=200&radius=5

Parameters

Name Type Default Description
entityId String Corresponds to the '_entity.id' or '*.label_entity_id' field, depending on the context.
asymId String Corresponds to the '_atom_site.label_asym_id' field.
authAsymId String Corresponds to the '_atom_site.auth_asym_id' field.
name String Residue name. Corresponds to the '_atom_site.label_comp_id' field.
authName String Author residue name. Corresponds to the '_atom_site.auth_comp_id' field.
insCode String Corresponds to the '_atom_site.pdbx_PDB_ins_code' field.
seqNumber Integer Residue seq. number. Corresponds to the '_atom_site.label_seq_id' field.
authSeqNumber Integer Author residue seq. number. Corresponds to the '_atom_site.auth_seq_id' field.
radius Float 5 Value in Angstroms.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _cell, _symmetry, _struct_conf, _struct_sheet_range, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Specific Residues /residues

Residues that satisfy the given parameters.

Example

/1cbs/residues?authAsymId=A&authName=REA&authSeqNumber=200

Parameters

Name Type Default Description
entityId String Corresponds to the '_entity.id' or '*.label_entity_id' field, depending on the context.
asymId String Corresponds to the '_atom_site.label_asym_id' field.
authAsymId String Corresponds to the '_atom_site.auth_asym_id' field.
name String Residue name. Corresponds to the '_atom_site.label_comp_id' field.
authName String Author residue name. Corresponds to the '_atom_site.auth_comp_id' field.
insCode String Corresponds to the '_atom_site.pdbx_PDB_ins_code' field.
seqNumber Integer Residue seq. number. Corresponds to the '_atom_site.label_seq_id' field.
authSeqNumber Integer Author residue seq. number. Corresponds to the '_atom_site.auth_seq_id' field.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Sidechain Atoms /sidechain

Atoms not named N, CA, C, O, P, OP1, OP2, O3', O5', C3', C4, C5' from polymer entities.

Example

/1cbs/sidechain

Parameters

Name Type Default Description
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Symmetry Mates /symmetryMates

Identifies symmetry mates within the given radius.

Example

/1cbs/symmetryMates?radius=5

Parameters

Name Type Default Description
radius Float 5 Value in Angstroms.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _cell, _symmetry, _struct_conf, _struct_sheet_range, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

C-Alpha/P Trace /trace

Atoms named CA and P from polymer entities + optionally HET and/or water atoms.

Example

/1cbs/trace?het=1

Parameters

Name Type Default Description
het Integer 0 If 1, include HET atoms.
water Integer 0 If 1, include water atoms.
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Water Atoms /water

Atoms from entities with type water.

Example

/1cbs/water

Parameters

Name Type Default Description
modelId String If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
atomSitesOnly Integer 0 If 1, only the '_atom_site' category is returned.
format String mmCIF Determines the output format (Currently supported: 'mmCIF').
encoding String cif Determines the output encoding (text based 'CIF' or binary 'BCIF').
lowPrecisionCoords Integer 0 If 1, stores coordinates with 1 digit instead of 3 digit precision (B-factors are stored with 1 digit precision instead of 2 when using the low precision).

Included mmCIF Categories

_entry, _entity, _exptl, _struct_conf, _struct_sheet_range, _pdbx_struct_assembly, _pdbx_struct_assembly_gen, _pdbx_struct_oper_list, _cell, _symmetry, _entity_poly, _struct_asym, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site

Generated for CoordinateServer 1.4.1, LiteMol Core 3.1.2 - April 12 2017