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, excludes s1
PyMOL> select vicinos, neighbor resi 10 |
| bound_to s1 | bto. s1 | Selects atoms directly bonded to s1, may include s1 |
| 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.