Selection Algebra

Selections can be made more precise or inclusive by combining them with logical operators, including the boolean and, or, and not. The boolean and selects only those items that have both (or all) of the named properties, and the boolean or selects items that have either (or any) of them. Venn diagrams show that and selects the areas of overlap, while or selects both areas.

See simple logic Venn diagram.

Selection Operator/Modifier Table

Selection operators and modifiers are listed below. The dummy variables s1 and s2 stand for selection-expressions such as "chain a" or "hydro."

Operator	Short form	Effect
not s1	!s1	Selects atoms that are not included in s1 PyMOL> select sidechains, ! bb
s1 and s2	s1 & s2	Selects atoms included in both s1 and s2 PyMOL> select far_bb, bb &farfrm_ten
s1 or s2	s1 | s2	Selects atoms included in either s1 or s2 PyMOL> select all_prot, bb | sidechain
s1 in s2	s1 in s2	Selects atoms in s1 whose identifiers name, resi, resn, chain and segi all match atoms in s2 PyMOL> select same_atms, pept in prot
s1 like s2	s1 l. s2	Selects atoms in s1 whose identifiers name and resi match atoms in s2 PyMOL> select similar_atms, pept like prot
s1 gap X		Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms. PyMOL> select farfrm_ten, resi 10 gap 5
s1 around X	s1 a. X	Selects atoms with centers within X Angstroms of the center of any atom in s1 PyMOL> select near_ten, resi 10 around 5
s1 expand X	s1 x. X	Expands s1 by all atoms within X Angstroms of the center of any atom in s1 PyMOL> select near_ten_x, near10 expand 3
s1 within X of s2	s1 w. X of s2	Selects atoms in s1 that are within X Angstroms of the s2 PyMOL> select bbnearten, bb w. 4 of resi 10
s1 near_to X of s2	s1 nto. X of s2	Same as within, but excludes s2 from the selection (and thus is identical to s1 and s2 around X)
s1 beyond X of s2	s1 be. X of s2	Selects atoms in s1 that are at least X Anstroms away from s2
byres s1	br. s1	Expands selection to complete residues PyMOL> select complete_res, br. bbnear10
bymolecule s1	bm. s1	Expands selection to complete molecules PyMOL> select complete_res, bm. bbnear10
byfragment s1	bf. s1	Expands selection to complete fragments PyMOL> select complete_res, bf. bbnear10
bysegment s1	bs. s1	Expands selection to complete segments PyMOL> select complete_res, bs. bbnear10
byobject s1	bo. s1	Expands selection to complete objects> PyMOL> select near_obj, bo. near_res
bycell s1		Expands selection to unit cell> PyMOL> select complete_cell, bycell orig_res
neighbor s1	nbr. s1	Selects atoms directly bonded to s1 PyMOL> select vicinos, neighbor resi 10
s1 extend X	s1 xt. X	Extends s1 by X bonds connected to atom in s1 PyMOL> select connect_x, near10 extend 3
pepseq SEQ	ps. SEQ	Selects peptide sequence matching upper-case one-letter sequence SEQ (see also FindSeq) PyMOL> select 1tvn and ps. FATEW

Comparison of distance operators

There are serveral very similar operators that select by pairwise atom distances. The following table lists the details how they differ.

Syntax 1: s1 operator X of s2
Syntax 2: s1 and (s2 operator X)

operator	distance is ...	measured from	includes s2	syntax	notes
near_to	≤ X	center	never	1	equivalent to "around"
within	≤ X	center	if matches s1	1
beyond	> X	center	never	1
gap	> X	center+vdw	never	2
around	≤ X	center	never	2	equivalent to "near_to"
expand	≤ X	center	always	2

Examples

Logical selections can be combined. For example, you might select atoms that are part of chain a, but not residue number 125:

# selects atoms that are part of chain a, but not residue number 125.
select chain a and (not resi 125)

# The following two selections are equivalent, 
select (name cb or name cg1 or name cg2) and chain A

# select c-beta's, c-gamma-1's and c-gamma-2's 
# that are in chain A.
select name cb+cg1+cg2 and chain A

# select all residues within 5 Ang. or any organic small molecules
select br. all within 5 of organic

# select helices
select ss 'h'

# select anything shown as a line
select rep lines

# select all residues with a b-factor less than 20, within 3 angstroms of any water
select br. b<20 & (all within 3 of resn HOH)

# select anything colored blue
select color blue

# select the 1st arginine
select first resn arg

# select 1foo's segment G's chain X's residue 444's alpha carbon
select 1foo/G/X/444/CA
# same thing
select 1foo and segi G and c. X and i. 444 and n. CA

# select the entire object that residue 23's beta caron is in:
select bo. i. 23 and n. CA

# select the molecule that chain C is in
select bm. c. C

Like the results of groups of arithmetic operations, the results of groups of logical operations depend on which operation is performed first. They have an order of precedence. To ensure that the operations are performed in the order you have in mind, use parentheses:

byres ((chain a or (chain b and (not resi 125))) around 5)

PyMOL will expand its logical selection out from the innermost parentheses.