Atom selection
Volatile and temporary selections
Selections can either be volatile, i.e. be used temporarily for the current command, or persistent, i.e. be used for the following commands. Persistent selections are made with the commands atoms select, angles select, distances select, peaks select, couplings select, rdc select, pcs select, and structures select. Selections made by other commands are always volatile.
General form
Atom selections are enclosed in double quotes and have the following general form:
Items in square brackets are optional and items in curly braces can occur zero or more times.
An atom selection can have the following elements:
- operator
- An operator to combine the selection that follows it with the previous selection
- atom
- An atom name, possibly containing wildcards ("?" or "*" replace exactly one or any number of characters, respectively)
- ~atom
- An atom name, possibly containing wildcards, as in the residue library, i.e. before a possible renaming with the library rename command
- &atomtype
- An atom type, possibly containing wildcards, as given in the residue library
- residue
- A residue selection, as explained below
- condition
- An additional condition, as explained below
Special atom names
The following special atom names can be used to select groups of atoms:
- AMIDE
- nitrogen atoms and hydrogen and pseudo atoms connected to nitrogens
- ASSIGNED
- atoms with assigned chemical shift values (in the first chemical shift list)
- BACKBONE
- main chain atoms (in proteins: N, CA, C)
- BB
- atoms whose position does not depend on side-chain torsion angles (in proteins: N, H, CA, HA, CB, C, O)
- CARBON
- carbon atoms
- CBOUND
- atoms covalently bound to carbon atoms
- HBOUND
- atoms covalently bound to hydrogen atoms
- HEAVY
- all atoms except hydrogen or pseudo atoms
- HYDROGEN
- hydrogen atoms
- HYDROXYL
- oxygen atoms and hydrogen and pseudo atoms connected to oxygens
- METHINE
- methine (CH1) groups, including the carbon and the hydrogen atom
- METHYL
- methyl (CH3) groups, including the carbon atom, three hydrogen atoms and the pseudo atom. In the case of isopropyl groups, e.g. in valine and leucine, the pseudo atom that represents both methyl groups is also selected.
- METHYLENE
- methylene (CH2) groups, including for each methylene group the carbon atom, two hydrogen atoms and the pseudo atom
- NBOUND
- atoms covalently bound to nitrogen atoms
- NH3
- NH3 groups, including for each NH3 group the nitrogen atom, three hydrogen atoms and the pseudo atom
- NITROGEN
- nitrogen atoms
- OBOUND
- atoms covalently bound to oxygen atoms
- OXYGEN
- oxygen atoms
- PBOUND
- atoms covalently bound to phosphorus atoms
- PHOSPHOR
- phosphorus atoms
- PSEUDO
- pseudo atoms
- RENAMED
- atoms for which an external name is defined
- SBOUND
- atoms covalently bound to sulfur atoms
- SELBOUND
- atoms bound to a selected atom
- SELECTED
- already selected atoms
- SULFUR
- sulfur atoms
- WITHCOORD
- atoms for which Cartesian coordinates are present
Residue selection
A residue selection consists of one or several of the following elements:
- @name
- a residue name, possibly containing wildcards
- @~name
- a residue name, possibly containing wildcards, as in the residue library, i.e. before a possible renaming with the library rename command
- @FIRST
- the first residue
- @LAST
- the last residue
- @first
- the first residue of every fragment with contiguous resi¬due numbers
- @last
- the last residue of every fragment with contiguous resi¬due numbers
- range
- a residue number range
Ranges of numbers in selections, e.g. residue number ranges, can be specified in one of the following ways:
- m
- a number
- m..n
- a range of numbers
- m-n
- alternative format for a range of numbers (only for n ≥ 0)
- m..
- from number m onwards
- m-
- from number m onwards; alternative format
- ..n
- from the first up to number n.
Operators
Atom selections can be combined using the following operators:
- =
- atoms in the new set (default)
- !
- atoms not in the new set
- +
- atoms in the current set or in the new set
- –
- atoms in the current set, but not in the new set
- /
- atoms in the current set and in the new set
Operators are always evaluated from left to right. The current atom set is the set of atoms defined by what precedes the operator. The new atom set is the set of atoms defined by what follows the operator. An empty atom selection selects all atoms.
Conditions
Additional conditions can be applied to atom selections:
- random=p
- Select randomly only a fraction p of all atoms that would normally be selected.
- shift=shiftmin..shiftmax
- Select only atoms with an assigned chemical shift value between shiftmin and shiftmax ppm in the first chemical shift list.
- tolerance=tolmin..tolmax
- Select only assigned atoms with a chemical shift tolerance value between tolmin and tolmax ppm in the first chemical shift list.
Examples
All atoms called HA:
HA
Atom HA of residue 5:
"HA 5"
All atoms called HA or whose name starts with HB:
"HA HB*"
Atoms HA in ALA residues with numbers 10-20:
"HA @ALA 10..20"
Atoms HA in ALA except in residues with numbers 10-20:
"HA @ALA - 10..20"
All atoms N, CA, C, and the side-chain heavy atoms of residues 15 and 17:
"N CA C + 15 17 - H* Q*"
The previous selection except for atoms whose starts with C:
"- C*"
Atoms in the previous selection that are bound to carbon atoms'
"/ CBOUND"
Assigned carbon atoms:
"CARBON / ASSIGNED"
Hydrogens and pseudo atoms, except hydroxyls and side-chain amides, whose atom type either starts with H_ or is PSEUD:
"H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD"
The commands atoms list and atoms select (with the parameter info=full) can be used to check atom selections.