1.4.9, powered by LiteMol
CoordinateServer is a fast, web-based tool for returning a subset of mmCIF coordinate data for a PDB entry held in the PDB archive. The server is able to return the specific portions of the structure that are relevant, as specified in your query. For example, the coordinates of the atoms within a 5Å radius around the ligand binding site, including symmetry mates. As a result, it greatly reduces the time needed to transmit and manipulate the data.
The server uses the text based CIF and binary BinaryCIF formats to deliver the data to the client. The server support is integrated into the LiteMol Viewer.
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=5Parameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/ambientResidues?entityId=&asymId=&authAsymId=&name=&authName=&insCode=&seqNumber=&authSeqNumber=&radius=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Assembly /assembly
Constructs assembly with the given id.
Example
/1e12/assembly?id=1Parameters
| 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, _entity_poly_seq, _pdbx_nonpoly_scheme, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/assembly?id=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Backbone Atoms /backbone
Atoms named N, CA, C, O, P, OP1, OP2, O3', O5', C3', C4, C5' from polymer entities.
Example
/1cbs/backboneParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/backbone?modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
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/cartoonParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/cartoon?modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Specific Chains /chains
Chains that satisfy the given parameters.
Example
/1cbs/chains?authAsymId=AParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/chains?entityId=&asymId=&authAsymId=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Specific Entities /entities
Entities that satisfy the given parameters.
Example
/1cbs/entities?type=polymerParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/entities?entityId=&type=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Full Structure /full
The full structure.
Example
/1cbs/fullParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _pdbx_nonpoly_scheme, _atom_site
Query Template
/PDBID/full?modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
HET Atoms /het
All non-water 'HETATM' records.
Example
/1cbs/hetParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/het?modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
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=5Parameters
| 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, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/ligandInteraction?entityId=&asymId=&authAsymId=&name=&authName=&insCode=&seqNumber=&authSeqNumber=&radius=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Residue Range /residueRange
Residues that satisfy the given parameters. Specify either [entityId + asymId + range] or [authAsymId + range]; if authAsymId is specified, entityId and asymId are ignored.
Example
/1cbs/residueRange?authAsymId=A&range=10-15:20-30Parameters
| 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. | |
| range | String | One or more sequence ranges (label_ or auth_ depending on which asymId is used; separated by :). Insertion codes can be included in the sequence number separted by space, i.e., '10 A-19'. | |
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/residueRange?entityId=&asymId=&authAsymId=&range=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Specific Residues /residues
Residues that satisfy the given parameters.
Example
/1cbs/residues?authAsymId=A&authName=REA&authSeqNumber=200Parameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/residues?entityId=&asymId=&authAsymId=&name=&authName=&insCode=&seqNumber=&authSeqNumber=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Sidechain Atoms /sidechain
Atoms not named N, CA, C, O, P, OP1, OP2, O3', O5', C3', C4, C5' from polymer entities.
Example
/1cbs/sidechainParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/sidechain?modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Symmetry Mates /symmetryMates
Identifies symmetry mates within the given radius.
Example
/1cbs/symmetryMates?radius=5Parameters
| 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, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/symmetryMates?radius=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
C-Alpha/P Trace /trace
Atoms named CA and P from polymer entities + optionally HET and/or water atoms.
Example
/1cbs/trace?het=1Parameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/trace?het=&water=&modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Water Atoms /water
Atoms from entities with type water.
Example
/1cbs/waterParameters
| 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, _entity_poly_seq, _struct_asym, _struct_conn, _struct_conn_type, _pdbx_struct_mod_residue, _chem_comp_bond, _atom_sites, _atom_site
Query Template
/PDBID/water?modelId=&atomSitesOnly=&format=&encoding=&lowPrecisionCoords=
Fill in PDBID and other parameters to customize the query.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
Empty-string values of parameters are ignored by the server, e.g. /entities?entityId=&type=water is the same as /entities?type=water. Names of residues/chains/entities/etc. are case sensitive.
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