Atom selection
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 con¬nected to nitrogens
- ASSIGNED
- atoms with assigned chemical shift values (in the first chemical shift list)
- BACKBONE
- main chain atoms (in proteins: N, Cα, C’)
- BB
- atoms whose position does not depend on side-chain tor¬sion angles (in proteins: N, H, C, H, C, 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 con¬nected to oxygens
- METHINE
- methine (CH1) groups, including the car¬bon and the hydrogen atom
- METHYL
- methyl (CH3) groups, including the car¬bon 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 car¬bon 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, as defined above
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=min..max
- Select only atoms with an assigned chemical shift value between min and max ppm in the first chemical shift list.
- tolerance=min..max
- Select only assigned atoms with a chemical shift tolerance value between min and max ppm in the first chemical shift list.
Examples
Examples of atom selections:
All atoms called HA:
HA
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" # HA in ALA of residues 10–20
"HA @ALA - 10..20" # HA in ALA except residues 10–20
"N CA C + 15 17 - H* Q*" # all N, CA, C, and side-chain heavy atoms in residues 15 and 17
"- C*" # the previous selection except atoms named C…
"/ CBOUND" # atoms in the previous selection that are bound to
# carbons
"CARBON / ASSIGNED" # assigned carbon atoms
"H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD"
# hydrogens and pseudo atoms, except hydroxyls and side-chain
# amides, whose atom type either starts with H_ or is PSEUD
The commands atom list and atom select (with the parameter info=full) can be used to check atom selections.