Editing Selection Algebra (section)

== 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."

{| class="wikitable"
|-
! Operator
! Aliases
! Description
|-
!colspan="3" style="text-align:left"| Generic
|-
| all || *
| All atoms currently loaded into PyMOL
|-
| none || 
| Empty selection
|-
| enabled || 
| Atoms from enabled objects
|-
!colspan="3" style="text-align:left"| Named selections
|-
| <span style="color: #999">sele</span> || 
| Named selection or object "sele", but only if it doesn't conflict with the name of another operator
|-
| %<span style="color: #999">sele</span> || 
| Named selection or object "sele" &nbsp; &nbsp; &nbsp; <span style="padding: 1px 4px; background-color: #fc3; border: 1px solid #ccc">Recommended, avoids ambiguity</span>
|-
| ?<span style="color: #999">sele</span> || 
| Named selection or object "sele", or empty selection if "sele" doesn't exist
|-
!colspan="3" style="text-align:left"| Logical
|-
| not <span style="color: #999">S1</span> || !
| Inverts selection
|-
| <span style="color: #999">S1</span> and <span style="color: #999">S2</span> || &
| Atoms included in both S1 and S2
|-
| <span style="color: #999">S1</span> or <span style="color: #999">S2</span> || <nowiki>|</nowiki>
| Atoms included in either S1 or S2
|-
| <span style="color: #999">S1 S2</span> ||
| implicit '''or'''
|-
| <span style="color: #999">S1</span> and (<span style="color: #999">S2</span> or <span style="color: #999">S3</span>) ||
| Parentheses for evaluation order control
|-
| first <span style="color: #999">S1</span> || 
| First atom in S1 (single atom selection)
|-
| last <span style="color: #999">S1</span> || 
| Last atom in S1 (single atom selection)
|-
!colspan="3" style="text-align:left"| Identifiers &nbsp; <small style="font-weight: normal">(see also [[Selection Macros]])</small>
|-
| model <span style="color: #999">1ubq</span> || m.
| Atoms from object "1ubq"
|-
| chain <span style="color: #999">C</span> || c.
| Chain identifier "C"
|-
| segi <span style="color: #999">S</span> || s.
| Segment identifier "S" ('''label_asym_id''' from mmCIF)
|-
| resn <span style="color: #999">ALA</span> || r.
| Residue name "ALA"
|-
| resi <span style="color: #999">100-200</span> || i.
| Residue identifier between 100 and 200
|-
| name <span style="color: #999">CA</span> || n.
| Atom name "CA"
|-
| alt <span style="color: #999">A</span> || 
| Alternate location "A"
|-
| index <span style="color: #999">123</span> || idx.
| Internal per-object atom index (changes with [[sort|sorting]])
|-
| id <span style="color: #999">123</span> || 
| ID column from PDB file
|-
| rank <span style="color: #999">123</span> || 
| Per-object atom index at load time (see also [[retain_order]])
|-
| pepseq <span style="color: #999">ACDEF</span> || ps.
| Protein residue sequence with one-letter code "ACDEF" (see also [[FindSeq]])
|-
| label <span style="color: #999">"Hello World"</span> || 
| Atoms with label "Hello World" ''(new in PyMOL 1.9)''
|-
!colspan="3" style="text-align:left"| Identifier matching
|-
| <span style="color: #999">S1</span> in <span style="color: #999">S2</span> || 
| Atoms in S1 whose identifiers ''name, resi, resn, chain'' and ''segi'' '''all''' match atoms in S2
|-
| <span style="color: #999">S1</span> like <span style="color: #999">S2</span> || 
| Atoms in S1 whose identifiers ''name'' and ''resi'' match atoms in S2
|-
!colspan="3" style="text-align:left"| Entity expansion
|-
|colspan="3" style="background-color: #fc3"| <span id="weak-by">Important:</span> All "by"-operators have a '''weak priority''', so (byres S1 or S2) is actually identical to (byres (S1 or S2)) and '''not''' to ((byres S1) or S2)
|-
| byobject <span style="color: #999">S1</span> || 
| Expands S1 to complete objects
|-
| bysegi <span style="color: #999">S1</span> || bs.
| Expands S1 to complete segments
|-
| bychain <span style="color: #999">S1</span> || bc.
| Expands S1 to complete chains
|-
| byres <span style="color: #999">S1</span> || br.
| Expands S1 to complete residues
|-
| bycalpha <span style="color: #999">S1</span> || bca.
| CA atoms of residues with at least one atom in S1
|-
| bymolecule <span style="color: #999">S1</span> || bm.
| Expands S1 to complete molecules (connected with bonds)
|-
| byfragment <span style="color: #999">S1</span> || bf.
| 
|-
| byring <span style="color: #999">S1</span> || 
| All rings of size ≤ 7 which have at least one atom in S1 ''(new in PyMOL 1.8.2)''
|-
| bycell <span style="color: #999">S1</span> || 
| Expands selection to unit cell
|-
!colspan="3" style="text-align:left"| Bond expansion
|-
| bound_to <span style="color: #999">S1</span> || bto.
| Atoms directly bonded to S1, may include S1
|-
| neighbor <span style="color: #999">S1</span> || nbr.
| Atoms directly bonded to S1, excludes S1
|-
| <span style="color: #999">S1</span> extend <span style="color: #999">3</span> || xt.
| Expands S1 by 3 bonds connected to atoms in S1
|-
!colspan="3" style="text-align:left"| Proximity &nbsp; <small style="font-weight: normal">(see also [[#Comparison of distance operators|comparison of distance operators]])</small>
|-
| <span style="color: #999">S1</span> within <span style="color: #999">12.3</span> of <span style="color: #999">S2</span> || w.
| Atoms in S1 that are within 12.3 Angstroms of any atom in S2
|-
| <span style="color: #999">S1</span> around <span style="color: #999">12.3</span> || a.
| Atoms with centers within 12.3 Angstroms of the center of any atom in S1
|-
| <span style="color: #999">S1</span> expand <span style="color: #999">12.3</span> || x.
| Expands S1 by atoms within 12.3 Angstroms of the center of any atom in S1
|-
| <span style="color: #999">S1</span> gap <span style="color: #999">1.2</span> || 
| Atoms whose VDW radii are separated from the VDW radii of S1 by a minimum of 1.2 Angstroms.
|-
| <span style="color: #999">S1</span> near_to <span style="color: #999">12.3</span> of <span style="color: #999">S2</span> || nto.
| Same as ''within'', but excludes S2 from the selection (and thus is identical to <code>S1 and S2 around 12.3</code>)
|-
| <span style="color: #999">S1</span> beyond <span style="color: #999">12.3</span> of <span style="color: #999">S2</span> || be.
| Atoms in S1 that are at least 12.3 Anstroms away from S2
|-
!colspan="3" style="text-align:left"| Properties
|-
| partial_charge <span style="color: #999">< 1.2</span> || pc.
| 
|-
| formal_charge <span style="color: #999">= 1</span> || fc.
| 
|-
| b <span style="color: #999">< 100.0</span> || 
| B-factor less than 100.0
|-
| q <span style="color: #999">< 1.0</span> || 
| Occupancy less than 1.0
|-
| ss <span style="color: #999">H+S</span> || 
| Atoms with secondary structure H (helix) or S (sheet)
|-
| elem <span style="color: #999">C</span> || e.
| Atoms of element C (carbon)
|-
| p<span style="color: #999">.foo</span> = <span style="color: #999">12</span> || 
| 
|-
| p<span style="color: #999">.foo</span> < <span style="color: #999">12.3</span> || 
| 
|-
| p<span style="color: #999">.foo</span> in <span style="color: #999">12+34</span> || 
| 
|-
| stereo <span style="color: #999">R</span> || 
| Chiral R/S stereo center with label R ''(only [https://pymol.org/d/media:stereochemistry Incentive PyMOL 1.4-1.8])''
|-
!colspan="3" style="text-align:left"| Flags
|-
| bonded || 
| Atoms which have at least one bond
|-
| protected ||
| see [[protect]]
|-
| fixed || fxd.
| see [[flag]]
|-
| restrained || rst.
| see [[flag]]
|-
| masked || msk.
| see [[mask]]
|-
| flag <span style="color: #999">25</span> || f.
| Atoms with flag 25, see [[flag]]
|-
!colspan="3" style="text-align:left"| Chemical classes
|-
| organic || org.
| Non-polymer organic compounds (e.g. ligands, buffers)
|-
| inorganic || ino.
| Non-polymer inorganic atoms/ions
|-
| solvent || sol.
| Water molecules
|-
| polymer || pol.
| Protein or Nucleic Acid
|-
| polymer.protein ||
| Protein ''(New in PyMOL 2.1)''
|-
| polymer.nucleic ||
| Nucleic Acid ''(New in PyMOL 2.1)''
|-
| guide || 
| Protein CA and nucleic acid C4*/C4'
|-
| hetatm || 
| Atoms loaded from PDB HETATM records
|-
| hydrogens || h.
| Hydrogen atoms
|-
| backbone || bb.
| Polymer backbone atoms ''(new in PyMOL 1.6.1)''
|-
| sidechain || sc.
| Polymer non-backbone atoms ''(new in PyMOL 1.6.1)''
|-
| metals || 
| Metal atoms ''(new in PyMOL 1.6.1)''
|-
| donors || don.
| Hydrogen bond donor atoms
|-
| acceptors || acc.
| Hydrogen bond acceptor atoms
|-
!colspan="3" style="text-align:left"| Style
|-
| visible || v.
| Atoms in enabled objects with at least one visible representation
|-
| rep <span style="color: #999">cartoon</span> || 
| Atoms with cartoon representation
|-
| color <span style="color: #999">blue</span> || 
| Atoms with atom-color blue (by color index)
|-
| cartoon_color <span style="color: #999">blue</span> || 
| Atoms with atom-level cartoon_color setting (by color index)
|-
| ribbon_color <span style="color: #999">blue</span> || 
| Atoms with atom-level ribbon_color setting (by color index)
|-
!colspan="3" style="text-align:left"| Non molecular
|-
| center || 
| Pseudo-atom at the center of the scene
|-
| origin || 
| Pseudo-atom at the origin of rotation
|-
!colspan="3" style="text-align:left"| Coordinates
|-
| state <span style="color: #999">123</span> || 
| Atoms with coordinates in state 123
|-
| present || pr.
| Atoms with coordinates in the current state
|-
| x <span style="color: #999">< 12.3</span> || 
| Atoms with model-space x coordinate less than 12.3
|-
| y <span style="color: #999">< 12.3</span> || 
| Atoms with model-space y coordinate less than 12.3
|-
| z <span style="color: #999">> 12.3</span> || 
| Atoms with model-space z coordinate greater than 12.3
|-
!colspan="3" style="text-align:left"| Atom typing
|-
| text_type <span style="color: #999">TT</span> || tt.
| ''Auto-assigned in [https://pymol.org/d/media:atomtyping Incentive PyMOL 1.4-1.8])''
|-
| numeric_type <span style="color: #999">123</span> || nt.
| 
|}