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 namedALA(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 |