Alphabetical List of Selection Operators

! – see not

| – see or

& – see and

a. – see around

acc. – see acceptors

acceptors - hydrogen bond acceptors

all – all atoms

al – see altloc

altloc – atoms with a given alternate location identifier

and – intersection (setwise AND) between two selections

around – atoms around a selection

bc. – see bychain

bca. – see bycalpha

be. – see beyond

beyond – atoms beyond a cutoff distance from a selection

bf. – see byfragment

bm. – see bymolecule

bo. – see byobject

bonded – atoms that participate in at least one bond

bound_to – atoms bound to a selection including those within the selection

br. – see byresidue

bs. – see bysegment

bto. – see bound_to

bycalpha – all C-alpha atoms from residues overlapped by a selection

bychain – all atoms in chains overlapped by a selection

byfrag – see byfragment

byfragment – all atoms in all fragments overlapped by a selection

bymol – see bymolecule

bymolecule – all atoms in all molecules overlapped by a selection

byobj – see byobject

byobject – all atoms in all objects overlapped by a selection

byres – see byresidue

byresi – see byresidue

byresidue – all atoms in all residues overlapped by a selection

byseg – see bysegment

bysegi – see bysegment

bysegment – all atoms in all segments overlapped by a selection

c. – see chain

cartoon_color – all atoms with a given cartoon_color atom setting

center – an imaginary atom located at the center of the viewer

chain – atoms with a given chain identifier

color – atoms with a given (atomic) color

don. – see donors

donors – hydrogen bond donors

e. – see element

elem – see element

element – atoms with a given element symbol

enabled – atoms in enabled objects

expand – atoms included and within a cutoff from a selection

extend – atoms included and within a certain number of bonds from a selection

f. – see flag

fc. – see formal_charge

first – the first atom in a given selection

flag – atoms with a numbered flag set

formal_charge – atoms with formal charge

gap – atoms with given gap between their van deer Waals spheres.

guide – atoms designated as residue guide atoms (flag 31)

h. – see hydrogens

hba. – see acceptors

hbd. – see donors

het – see hetatm

hetatm – atoms designated as PDB HETATMs.

hydro – see hydrogens

hydrogens – hydrogen atoms

i. – see residue

id – atoms with a given identifier number (e.g. PDB or MOL file atom identifier)

idx. – see index

in – atoms matching certain identifiers in another selection

index – atoms with a given PyMOL internal index (1-based)

ino. – see inorganic

inorganic – atoms in molecules that do not contain carbon.

l. – see like

last – the last atom in a given selection

like – atoms matching certain identifiers in another selection

m. – see object

model – see object

n. – see name

name – atoms matching a given name

nbr. – see neighbor

near_to – atoms not included but within the vicinity of a selection

neighbor – atoms bound to but not including those within the selection

none – an empty selection

not – all atoms not in a selection

nt. – see numeric_type

nto. – see near_to

numeric_type – atoms with a given numeric type

o. – see object

object – atoms within a given object-name-pattern

or – union (setwise OR) between two selections

org. – see organic

organic – atoms contained in carbon-containing molecules that are not known polymers.

origin

partial_charge

pc.

pepseq

pol.

polymer

pr.

present

ps.

r.

rank

rep

resi – see resident

resid – see resident

resident – residue identifier (usually numerical)

residue – see resident

resn

resname

ribbon_color

s.

segi

segid

sol.

solvent

ss

state

symbol – see element

text_type

tt.

v.

visible

w.

within

x.

xt.

ymolecule

b

q