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MolViewSpec selectors

Selectors are used in MVS to define substructures (components) and apply colors, labels, or tooltips to them. MVS nodes that take a selector parameter are component (creates a component from the parent structure node) and color (applies coloring to a part of the parent representation node).

There are three kinds of selectors:

  • Static selector is a string that selects a part of the structure based on entity type. The supported static selectors are these:

    "all", "polymer", "protein", "nucleic", "branched", "ligand", "ion", "water"

  • Component expression is an object that selects a set of atoms based on their properties like chain identifier, residue number, or type symbol. The type of a component expression object is:

    {
    label_entity_id?: str,    // Entity identifier
    label_asym_id?: str,      // Chain identifier in label_* numbering
    auth_asym_id?: str,       // Chain identifier in auth_* numbering
    label_seq_id?: int,       // Residue number in label_* numbering
    auth_seq_id?: int,        // Residue number in auth_* numbering
    pdbx_PDB_ins_code?: str,  // PDB insertion code
    beg_label_seq_id?: int,   // Minimum label_seq_id (inclusive), leave blank to start from the beginning of the chain
    end_label_seq_id?: int,   // Maximum label_seq_id (inclusive), leave blank to go to the end of the chain
    beg_auth_seq_id?: int,    // Minimum auth_seq_id (inclusive), leave blank to start from the beginning of the chain
    end_auth_seq_id?: int,    // Maximum auth_seq_id (inclusive), leave blank to go to the end of the chain
    label_atom_id?: str,      // Atom name like 'CA', 'N', 'O', in label_* numbering
    auth_atom_id?: str,       // Atom name like 'CA', 'N', 'O', in auth_* numbering
    type_symbol?: str,        // Element symbol like 'H', 'HE', 'LI', 'BE'
    atom_id?: int,            // Unique atom identifier (_atom_site.id)
    atom_index?: int,         // 0-based index of the atom in the source data
    instance_id?: str         // Instance identifier to distinguish instances of the same chain created by applying different symmetry operators, like 'ASM-X0-1' for assemblies or '1_555' for crystals
}

    A component expression can include any combination of the fields. An expression with multiple fields selects atoms that fulfill all fields at the same time. Examples:

    // Select whole chain A
selector: { label_asym_id: 'A' }

// Select residues 100 to 200 (inclusive) in chain B
selector: { label_asym_id: 'B', beg_label_seq_id: 100, end_label_seq_id: 200 }

// Select C-alpha atoms in residue 100 (using auth_* numbering) of any chain
selector: { auth_seq_id: 100, type_symbol: 'C', auth_atom_id: 'CA' }

  • Union component expression is an array of simple component expressions. A union component expression is interpreted as set union, i.e. it selects all atoms that fulfill at least one of the expressions in the array. Example:

    // Select chains A, B, and C
selector: [{ label_asym_id: 'A' }, { label_asym_id: 'B' }, { label_asym_id: 'C' }];

// Select residues up to 100 (inclusive) in chain A plus all magnesium atoms
selector: [{ label_asym_id: 'A', end_label_seq_id: 100 }, { type_symbol: 'MG' }];

instance_id

The instance_id field in component expressions does not refer to any column in mmCIF atom_site category, but can be used distinguish instances of the same chain created by applying different symmetry operators. Instance IDs follow these rules:

Crystals

Instances created by crystal (spacegroup) symmetry use IDs in the form n_klm, in accordance with the mmCIF dictionary recommendation. However, to avoid any ambiguities, any translation index (k, l, m) smaller than 0 or greater than 9 is always enclosed in parenthesis. Indices 0–9 never use parentheses.

  • e.g. 1_555, 2_454
  • e.g. 1_(11)15, 1_1(11)5, 1_11(15) (instead of ambiguous 1_1115)
  • e.g. 1_(-1)1(-1)

Assemblies

Instances in assemblies use IDs inspired by the wwPDB recommendation for naming chains in assemblies. Instance IDs are based on data from pdbx_struct_assembly_gen and pdbx_struct_oper_list categories in mmCIF dictionary.

Where only one operator is applied to create the instance, the instance ID is ASM- plus the operator identifier (pdbx_struct_oper_list.id).

  • e.g. ASM-1, ASM-2, ASM-3, ASM-4 from generator expression 1,2,3,4
  • e.g. ASM-1, ASM-2, ASM-3, ASM-4, ASM-5 from generator expression (1-5)

Where multiple operators are applied to create the instance, the instance ID is ASM- plus a dash-separated list of operator identifiers. The order of the operators is the same as in the generator expression (i.e. rightmost operator is applied first).

  • e.g. ASM-X0-1, ASM-X0-2... ASM-X0-20 from generator expression (X0)(1-20)
  • e.g. ASM-1-61, ASM-1-62... ASM-2-61, ASM-2-62... ASM-60-88 from generator expression (1-60)(61-88)

ref

Component expressions can be applied to primitives as well. Furthermore, a ref can be provided to make selections with a specific node when working e.g. with multiple structures. Any MVS node allows you to set an anchor:

builder.download(url=url).parse(format="mmcif").model_structure(ref="X")

This ref can then be referenced in the context of a selection:

PrimitiveComponentExpressions(structure_ref="X", expressions=[ComponentExpression(auth_seq_id=508)])

An alternative to using selectors is using MVS annotations. This means defining the selections in a separate file and referencing them from the MVS file.