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`
polarh	polar hydrogens	`polarh`
nonpolarh	non-polar hydrogens	`not nonpolarh`
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`