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:

"[operator] {atom} [residue] {condition} {operator {atom} [residue] {condition}}"

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.