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Target Specification in Chimera2 versus Chimera1

In this page, “Chimera1” 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; thus, some of the examples don't work.

Example Translations from Chimera1 to Chimera2

The following specify atoms N, CA, C, O in chain A residues 14-39 and in chain B residues 55-65. Chimera2 requires an intersection (&) because chain is in the hierarchy above residue (repeated use of the chain symbol / “resets” the successive narrowing of the specification):

Chimera1   :14-39.a,55-65.b@n,ca,c,o

Chimera2   /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.

Chimera1   :14-39.a:55-65.b@n,ca,c,o

Chimera2   /a:14-39/b:55-65@n,ca,c,o

In Chimera1, & (intersection) has priority over | (union), but Chimera2 allows using parentheses to make it clearer. Note also the use of :: for residue attribute:

Chimera1  Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2

Chimera2  Ng+ | N3+ | N2+ | O2- | O3- | (::amberName=HIP & @nd1,ne2)

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

Chimera1  @ca/bfactor>40

Chimera2  @ca & @@bfactor>40

Some Chimera2 specifications have no exact Chimera1 equivalent because the desired order of operations could not be enforced without parentheses. For example, Chimera2 allows either of the following:

Chimera2 command:   rlabel strand & (aromatic :< 4.5)

Chimera2 command:   rlabel (strand & aromatic) :< 4.5

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 Chimera1:

Chimera1 command:   rlabel strand & aromatic zr<4.5

The second of the Chimera2 examples above could be achieved with a multistep process in Chimera1:

Chimera1 command:   select strand & aromatic

Chimera1 command:   namesel sel1

Chimera1 command:   ~select

Chimera1 command:   rlabel sel1 zr<4.5

UCSF Resource for Biocomputing, Visualization, and Informatics / August 2015