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selection:alpha

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
selection/alpha.txt · Last modified: 2013/08/19 21:01 (external edit)