Target Specification in ChimeraX versus Chimera

In this page, “Chimera” is used to denote UCSF Chimera. See also: ChimeraX command-line target specification

• ChimeraX basic hierarchy: atomic model ↔ chain ↔ residue ↔ atom
  (Chimera hierarchy: model.submodel ↔ residue.chain ↔ atom.altloc)
• the model level can have any number of sublevels (model numbers N.N.N, N.N.N.N, etc. are possible)
• residues and atoms do not have sublevels
• atom, residue, and model attribute specifications are signaled by @@, ::, and ##, respectively, and are treated separately from hierarchical specifiers
  (Chimera uses @/, :/, and #/ and treats them as a further restriction in the hierarchy)
• there is no separate set of Boolean operators for combining attributes; instead the main set of operators (& | ~) can be used to achieve the same results
• parentheses are allowed
• embedded spaces are allowed, and commands cannot require adjacent specifications without an intervening keyword
• zone specifications use @ instead of za and : instead of zr or z; a model level # and comparators <=, >= have been added

Example Translations from Chimera to ChimeraX

The following specify atoms N, CA, C, O in chain A residues 14-39 and in chain B residues 55-65. ChimeraX requires an intersection (&) because chain is in the hierarchy above residue (repeated use of the chain symbol / “resets” the successive narrowing of the specification):

Chimera   :14-39.a,55-65.b@n,ca,c,o

ChimeraX   /a:14-39/b:55-65 & @n,ca,c,o

The following specify atoms N, CA, C, O in chain B residues 55-65, plus all atoms in chain A residues 14-39.

Chimera   :14-39.a:55-65.b@n,ca,c,o

ChimeraX   /a:14-39/b:55-65@n,ca,c,o

In Chimera, & (intersection) has priority over | (union), but ChimeraX allows using parentheses to make it clearer. Note also the use of :: for residue attribute:

Chimera  Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2

ChimeraX  Ng+ | N3+ | N2+ | O2- | O3- | (::amber_name=HIP & @nd1,ne2)

(The amber_name residue attribute is generated by running addcharge).

In ChimeraX, attributes are treated as separate selectors rather than part of the hierarchy, so combination symbols are required:

Chimera  @ca/bfactor>40

ChimeraX  @ca & @@bfactor>40

Some ChimeraX specifications have no exact Chimera equivalent because the desired order of operations could not be enforced without parentheses. For example, ChimeraX allows either of the following:

ChimeraX command:   label strand & (aromatic :< 4.5) residues

ChimeraX command:   label (strand & aromatic) :< 4.5 residues

The first would label residues in β-strand with any atom less than 4.5 Å from an aromatic residue. The second would label residues with any atom less than 4.5 Å from residues that are both aromatic and in β-strand. Only the first could be achieved directly in Chimera:

Chimera command:   rlabel strand & aromatic zr<4.5

The second of the ChimeraX examples above could be achieved with a multistep process in Chimera:

Chimera command:   select strand & aromatic

Chimera command:   namesel sel1

Chimera command:   ~select

Chimera command:   rlabel sel1 zr<4.5