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
- byres – see byresidue
- byresi – see byresidue
- byseg – see bysegment
- bysegi – see bysegment
- 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
- 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)
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