Selection Language
Selections (or 'Sele' for short) strings can be input at various places in the user interface or when scripting. They are used to limit which atoms/residues are shown in a [molecular representation]{@tutorial molecular-representations} or what atoms are loaded from a trajectory.
Example
Select the side-chain and C-alpha atoms plus the backbone nitrogen in case of proline. not backbone or .CA or (PRO and .N) This selection is useful to display the sidechains together with a backbone trace. Hence there is also the keyword sidechainAttached for it.
Language
Keywords
- all, *
- sidechain
- sidechainAttached (
not backbone or .CA or (PRO and .N)) - backbone
- protein
- nucleic
- rna
- dna
- hetero
- ligand (
( not polymer or hetero ) and not ( water or ion )) - ion
- saccharide/sugar
- polymer
- water
- hydrogen
- helix
- sheet
- turn (
not helix and not sheet) - small (
Gly or Ala or Ser) - nucleophilic (
Ser or Thr or Cys) - hydrophobic (
Ala or Val or Leu or Ile or Met or Pro or Phe or Trp) - aromatic (
Phe or Tyr or Trp or His) - amid (
Asn or Gln) - acidic (
Asp or Glu) - basic (
His or Lys or Arg) - charged (
Asp or Glu or His or Lys or Arg) - polar (
Asp or Cys or Gly or Glu or His or Lys or Arg or Asn or Gln or Ser or Thr or Tyr) - nonpolar (
Ala or Ile or Leu or Met or Phe or Pro or Val or Trp) - cyclic (
His or Phe or Pro or Trp or Tyr) - aliphatic (
Ala or Gly or Ile or Leu or Val) - bonded (all atoms with at least one bond)
- ring (all atoms within rings)
Expressions
- residue number: 1, 2, 100
- residue number range: 3-40 (Note that around the dash - no spaces are allowed)
- chain name: :A
- atom name: .CA, .C, .N, ...
- model: /0, /1, ...
- residue name: ALA, GLU, SOL, DMPC, ...
- numeric residue name: [032], [1AB], ...
- list of residue names: [ALA,GLU,MET], [ARG,LYS], ...
- element name: _H, _C, _O, ...
- alternate location: %A, %B, ... or % for non-alternate location atoms
- insertion code: ^A, ^B, ... or ^ for residues with no insertion code
Some of these expressions can be combined (in this order) - residue numer (range), insertion code, chain name, atom name, alternate location, model - like this
// select C-alpha atoms of residue 10 with insertion code A
// from chain F in model 0 at alternate location C
10^A:F.CA%C/0
which is the same as
10 and ^A and :F and .CA and %C and /0
Single expressions may be left out as long as the order (see above) is kept, for example:
:A/0 # select chain A from model 0
Atomindex
A list of atom indices can be given as a comma seperated list (no spaces in between) prefixed with the @ character.
@0,1,4,5,11,23,42
Logical operators (in order of binding strength)
- NOT
- AND
- OR
Additionally, parentheses () can be used for grouping: :A and ( 1 or 10 or 100 ) # select residues 1, 10 and 100 from chain A