Selection Language

Miew allows to view different molecule parts (subsets of atoms) using specific visualizations. To select these subsets one should use a Selection Language; its syntax is described below.

Quick Examples

  • chain A and not hetatm
    select all atoms in chain A except for HETATM PDB records.
  • residue ALA
    select all residues named ALA (alanine).
  • serial 1:10, 20:30 and type C, N
    select Carbon and Nitrogen atoms with atom indices in range 1 through 10 or 20 through 30 inclusively.

Syntax

An Expression in Miew selection language consists of a Selector or a set of Expressions joined with logical operations AND, OR, NOT and brackets for grouping.

Expression ::=
  Selector |
  Expression 'AND' Expression |
  Expression 'OR' Expression |
  'NOT' Expression |
  '(' Expression ')'

Selector consists of a keyword followed by an optional comma separated parameter list. Some keywords accept integer parameters (e.g. atom or residue indices), others accept strings (e.g. atom or residue names). Keywords are case insensitive.

Integer parameter can be a single value or range of values, where range borders are delimited by a colon. Example: 3:7 defines an integer range: 3, 4, 5, 6, and 7).

String parameters should be flanked by quotation marks unless the string consists of letters, digits and underscores only.

Selector ::=
  Keyword |
  Keyword IntegerList |
  Keyword StringList

IntegerList ::= Range | IntegerList ',' Range
Range ::= Number | Number ':' Number

StringList ::= String | StringList ',' String
String ::= AlphaNumericString | QuotedString

Keywords list

Keyword Description Example
all all atoms all
none empty subset none
hetatm atoms defined as HETATM in PDB-file not hetatm
water water residues (WAT, HOH, H2O) hetatm and not water
serial int atoms by serial numbers serial 1:10, 13, 25:37
name str atoms by names name CA, CB
elem str atoms by chemical elements elem O, N, H
type str deprecated! superseded by elem  
altloc str atoms by alternative location (conformation) altloc " ", A
residue str residues by names residue ALA, CYS
sequence int residues by indices in a sequence sequence 35:37
residx int residues by ordinal index residx 1327
icode str residues by insertion code sequence 409 and icode B
protein one of 22 common amino acid residues  
basic basic amino acid residue: ARG, HIS, LYS  
acidic acidic amino acid residue: ASP, GLU  
charged basic or acidic residue  
polar polar amino acid residue: ASN, CYS, GLN, SER, THR, TYR  
nonpolar non-polar amino acid residue: ALA, ILE, LEU, MET, PHE, PRO, TRP, VAL  
aromatic aromatic amino acid residue: PHE, TRP, TYR  
nucleic nucleic residue  
purine purine nucleic residue: A, G, I and variations  
pyrimidine pyrimidine nucleic residue: C, T, U and variations  
chain str chain by name chain A, C, E