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Target Specification in ChimeraX versus Chimera

In this page, “Chimera” is used to denote UCSF Chimera. Like the main target specification page, this page describes a planned scheme, some of which is not yet implemented.

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- | (::amberName=HIP & @nd1,ne2)
(however, example is only hypothetical since there is no amberName residue attribute in ChimeraX)

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

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2018