3. Selection commands

Once you have the Universe() object, you can select atoms (using a syntax very similar to CHARMM’s atom selection syntax):

>>> kalp = universe.select_atoms("segid KALP")

The select_atoms() method of a AtomGroup or a Universe returns a AtomGroup, so you can use all the methods defined for AtomGroups on them. Selections always return an AtomGroup with atoms sorted according to their index in the topology (this is to ensure that there are not any duplicates, which can happen with complicated selections).

One can group subselections using parentheses:

>>> universe.select_atoms("segid DMPC and not (name H* or type OW)")
<AtomGroup with 3420 atoms>

Almost all the basic CHARMM selections work.

It is also possible to export selections for external software packages with the help of Selection exporters.

3.1. Selection Keywords

The following describes all selection keywords currently understood by the selection parser. The following applies to all selections:

  • Keywords are case sensitive.

  • Atoms are automatically sequentially ordered in a resulting selection (see notes below on Ordered selections for how to circumvent this if necessary).

  • Selections are parsed left to right and parentheses can be used for grouping.

  • Currently, only “stemming” is implemented as a primitive form of pattern matching: Using the * character in a string such as GL* selects all strings that start with “GL” such as “GLU”, “GLY”, “GLX29”, “GLN”.

3.1.1. Simple selections

protein, backbone, nucleic, nucleicbackbone

selects all atoms that belong to a standard set of residues; a protein is identfied by a hard-coded set of residue names so it may not work for esoteric residues.

segid seg-name

select by segid (as given in the topology), e.g. segid 4AKE or segid DMPC

resid residue-number-range

resid can take a single residue number or a range of numbers. A range consists of two numbers separated by a colon (inclusive) such as resid 1:5. A residue number (“resid”) is taken directly from the topology.

resnum resnum-number-range

resnum is the canonical residue number; typically it is set to the residue id in the original PDB structure.

resname residue-name

select by residue name, e.g. resname LYS

name atom-name

select by atom name (as given in the topology). Often, this is force field dependent. Example: name CA (for C&alpha; atoms) or name OW (for SPC water oxygen)

type atom-type

select by atom type; this is either a string or a number and depends on the force field; it is read from the topology file (e.g. the CHARMM PSF file contains numeric atom types). It has non-sensical values when a PDB or GRO file is used as a topology.

atom seg-name residue-number atom-name

a selector for a single atom consisting of segid resid atomname, e.g. DMPC 1 C2 selects the C2 carbon of the first residue of the DMPC segment

altloc alternative-location

a selection for atoms where alternative locations are available, which is often the case with high-resolution crystal structures e.g. resid 4 and resname ALA and altloc B selects only the atoms of ALA-4 that have an altloc B record.

moltype molecule-type

select by molecule type, e.g. moltype Protein_A. At the moment, only the TPR format defines the molecule type.

3.1.2. Boolean

not

all atoms not in the selection, e.g. not protein selects all atoms that aren’t part of a protein

and, or

combine two selections according to the rules of boolean algebra, e.g. protein and not (resname ALA or resname LYS) selects all atoms that belong to a protein, but are not in a lysine or alanine residue

3.1.3. Geometric

around distance selection

selects all atoms a certain cutoff away from another selection, e.g. around 3.5 protein selects all atoms not belonging to protein that are within 3.5 Angstroms from the protein

sphlayer innerRadius externalRadius selection

selects all atoms within a spherical layer centered in the center of geometry (COG) of a given selection, e.g., sphlayer 2.4 6.0 ( protein and ( resid 130 or resid 80 ) ) selects the center of geometry of protein, resid 130, resid 80 and creates a spherical layer of inner radius 2.4 and external radius 6.0 around the COG.

sphzone externalRadius selection

selects all atoms within a spherical zone centered in the center of geometry (COG) of a given selection, e.g. sphzone 6.0 ( protein and ( resid 130 or resid 80 ) ) selects the center of geometry of protein, resid 130, resid 80 and creates a sphere of radius 6.0 around the COG.

cylayer innerRadius externalRadius zMax zMin selection

selects all atoms within a cylindric layer centered in the center of geometry (COG) of a given selection, e.g. cylayer 5 10 10 -8 protein selects the center of geometry of protein, and creates a cylindrical layer of inner radius 5, external radius 10 centered on the COG. In z, the cylinder extends from 10 above the COG to 8 below. Positive values for zMin, or negative ones for zMax, are allowed.

cyzone externalRadius zMax zMin selection

selects all atoms within a cylindric zone centered in the center of geometry (COG) of a given selection, e.g. cyzone 15 4 -8 protein and resid 42 selects the center of geometry of protein and resid 42, and creates a cylinder of external radius 15 centered on the COG. In z, the cylinder extends from 4 above the COG to 8 below. Positive values for zMin, or negative ones for zMax, are allowed.

Changed in version 0.10.0: keywords cyzone and cylayer now take zMax and zMin to be relative to the COG of selection, instead of absolute z-values in the box.

point x y z distance

selects all atoms within a cutoff of a point in space, make sure coordinate is separated by spaces, e.g. point 5.0 5.0 5.0 3.5 selects all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0)

prop [abs] property operator value

selects atoms based on position, using property x, y, or z coordinate. Supports the abs keyword (for absolute value) and the following operators: <, >, <=, >=, ==, !=. For example, prop z >= 5.0 selects all atoms with z coordinate greater than 5.0; prop abs z <= 5.0 selects all atoms within -5.0 <= z <= 5.0.

From version 0.6 onwards, some geometric selections (around, sphlayer, sphzone, point) can use a k-d tree based, fast search algorithm (about three times faster than the previous version). However, it does not take periodicity into account. The fast algorithm is the default for around. Periodicity is only taken into account with the distance_array() functions via a minimum image convention (and this only works for rectangular simulation cells). If periodic boundary conditions should be taken into account then change the default behaviour of MDAnalysis by setting these two flags:

MDAnalysis.core.flags['use_periodic_selections'] = True
MDAnalysis.core.flags['use_KDTree_routines'] = False

3.1.4. Similarity and connectivity

same subkeyword as selection

selects all atoms that have the same subkeyword value as any atom in selection. Allowed subkeyword values are the atom properties: name, type, resname, resid, segid, mass, charge, radius, bfactor, resnum, the groups an atom belong to: residue, segment, fragment, and the atom coordinates x, y, z.

byres selection

selects all atoms that are in the same segment and residue as selection, e.g. specify the subselection after the byres keyword. byres is a shortcut to same residue as

bonded selection

selects all atoms that are bonded to selection eg: select name H and bonded name O selects only hydrogens bonded to oxygens

3.1.5. Index

bynum index-range

selects all atoms within a range of (1-based) inclusive indices, e.g. bynum 1 selects the first atom in the universe; bynum 5:10 selects atoms 5 through 10 inclusive. All atoms in the MDAnalysis.Universe are consecutively numbered, and the index runs from 1 up to the total number of atoms.

index index-range

selects all atoms within a range of (0-based) inclusive indices, e.g. index 0 selects the first atom in the universe; index 5:10 selects atoms 6 through 11 inclusive. All atoms in the MDAnalysis.Universe are consecutively numbered, and the index runs from 0 up to the total number of atoms - 1.

3.1.6. Preexisting selections and modifiers

group group-name

selects the atoms in the AtomGroup passed to the function as an argument named group-name. Only the atoms common to group-name and the instance select_atoms() was called from will be considered, unless group is preceded by the global keyword. group-name will be included in the parsing just by comparison of atom indices. This means that it is up to the user to make sure the group-name group was defined in an appropriate Universe.

global selection

by default, when issuing select_atoms() from an AtomGroup, selections and subselections are returned intersected with the atoms of that instance. Prefixing a selection term with global causes its selection to be returned in its entirety. As an example, the global keyword allows for lipids.select_atoms("around 10 global protein") — where lipids is a group that does not contain any proteins. Were global absent, the result would be an empty selection since the protein subselection would itself be empty. When issuing select_atoms() from a Universe, global is ignored.

Deprecated since version 0.11: The use of fullgroup has been deprecated in favor of the equivalent global group.

3.2. Dynamic selections

By default select_atoms() returns an AtomGroup, in which the list of atoms is constant across trajectory frame changes. If select_atoms() is invoked with named argument updating set to True, an UpdatingAtomGroup instance will be returned instead. It behaves just like an AtomGroup object, with the difference that the selection expressions are re-evaluated every time the trajectory frame changes (this happens lazily, only when the UpdatingAtomGroup object is accessed so that there is no redundant updating going on):

# A dynamic selection of corner atoms:
>>> ag_updating = universe.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True)
>>> ag_updating
<UpdatingAtomGroup with 9 atoms>
>>> universe.trajectory.next()
>>> ag_updating
<UpdatingAtomGroup with 14 atoms>

Using the group selection keyword for preexisting-selections, one can make updating selections depend on AtomGroup, or even other UpdatingAtomGroup, instances. Likewise, making an updating selection from an already updating group will cause later updates to also reflect the updating of the base group:

>>> chained_ag_updating = ag_updating.select_atoms("resid 1:1000", updating=True)
>>> chained_ag_updating
<UpdatingAtomGroup with 3 atoms>
>>> universe.trajectory.next()
>>> chained_ag_updating
<UpdatingAtomGroup with 7 atoms>

Finally, a non-updating selection or a slicing/addition operation made on an UpdatingAtomGroup will return a static AtomGroup, which will no longer update across frames:

>>> static_ag = ag_updating.select_atoms("resid 1:1000")
>>> static_ag
<UpdatingAtomGroup with 3 atoms>
>>> universe.trajectory.next()
>>> static_ag
<UpdatingAtomGroup with 3 atoms>

3.3. Instant selectors

Deprecated since version 0.16.2: Instant selectors will be removed in the 1.0 release in order to streamline the MDAnalysis user interface. They do not seem to be widely used anymore, can produce cryptic error messages, and are not considered “Pythonic” (and therefore not very intuitive for new users). See issue #1377 for more details.

For interactive work it becomes rather tedious to type common selection strings repeatedly. MDAnalysis automatically generates a number of instant selectors as attributes of the Universe and number of other levels of the structural hierarchy, namely for AtomGroup, Residue, ResidueGroup, Segment and SegmentGroup.

3.3.1. Segment selector

Deprecated since version 0.16.2: Use SegmentGroup[SegmentGroup.segids == '<name>'] instead. Note that this always returns a SegmentGroup and never a Segment (unlike the instant selector).

  • universe.<segid> or universe.s<segid> (if <segid> starts with a number)

  • returns a Segment

  • works for Universe and SegmentGroup

  • example
    >>> u.s4AKE
<Segment '4AKE'>

3.3.2. Resid selector

Deprecated since version 0.16.2: Use Segment.residues[N-1] instead.

  • seg.r<N> selects residue with number <N>

  • returns a Residue

  • works for Segment and SegmentGroup

  • example
    >>>  u.s4AKE.r100
<Residue 'GLY', 100>

3.3.3. Residue name selector

Deprecated since version 0.16.2: Use ResidueGroup[ResidueGroup.resnames == '<name>'] or Segment.residues[Segment.residues == '<name>'] instead. Note that this always returns a ResidueGroup and never a Residue (unlike the instant selector).

  • seg.<resname> selects residues with residue name <resname>

  • returns a ResidueGroup

  • works for Segment and SegmentGroup

  • examples
    >>> u.s4AKE.MET
<ResidueGroup [<Residue 'MET', 1>, <Residue 'MET', 21>, <Residue 'MET', 34>, <Residue 'MET', 53>, <Residue 'MET', 96>, <Residue 'MET', 174>]>
>>> u.s4AKE.CYS
<ResidueGroup [<Residue 'CYS', 77>]>
>>> u.s4AKE.TRP
NoDataError: No atoms defined for AtomGroup

  • The result is always a ResidueGroup; if no residues can be found then a MDAnalysis.NoDataError is raised.

3.3.4. Atom name selector

Deprecated since version 0.16.2: Use AtomGroup.select_atoms('name <name>') instead. Note that this always returns an AtomGroup and never an Atom (unlike the instant selector).

  • g.<atomname> selects a single atom or a group of atoms with name <atomname>

  • returns

    • a Atom if only a single atom was found,

    • a AtomGroup if more than one atom was found, or

    • raises a MDAnalysis.SelectionError if no atom was found.

  • works for any group derived from AtomGroup (i.e. all the ones mentioned above)

  • examples
    >>> u.atoms.CG
>>> <AtomGroup with 125 atoms>
>>> u.s4AKE.CG
<AtomGroup with 125 atoms>
>>> u.s4AKE.r100.CA
< Atom 1516: name 'CA' of type '23' of resname 'GLY', resid 100 and segid '4AKE'>
>>> u.s4AKE.r100.CB
SelectionError: No atom in residue GLY with name CB

3.4. Ordered selections

select_atoms() sorts the atoms in the AtomGroup by atom index before returning them (this is to eliminate possible duplicates in the selection). If the ordering of atoms is crucial (for instance when describing angles or dihedrals) or if duplicate atoms are required then one has to concatenate multiple AtomGroups, which does not sort them.

The most straightforward way to concatentate two AtomGroups is by using the + operator:

>>> ordered = u.select_atoms("segid DMPC and resid 3 and name P") + u.select_atoms("segid DMPC and resid 2 and name P")
>>> print list(ordered)
[< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>,
< Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>]

A shortcut is to provide two or more selections to select_atoms(), which then does the concatenation automatically:

>>> print list(universe.select_atoms("segid DMPC and resid 3 and name P", "segid DMPC and resid 2 and name P"))
[< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>,
< Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>]

Just for comparison to show that a single selection string does not work as one might expect:

# WRONG!
>>> print list(universe.select_atoms("segid DMPC and ( resid 3 or resid 2 ) and name P"))
[< Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>,
< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>]