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Command: select

A selection specifies items (models or their parts) for subsequent operations; the selected items are highlighted with green outlines in the graphics window. The select command can:

For click-to-select, see mousemode. See also: selection vs. specification, the Select menu

New Selection

Usage: select  spec  [ residues  true | false ] [ polymer  chain-spec ] [ minimumLength  min ] [ maximumLength  max ]

The top-level select command replaces any previous selection with a new one containing the specified items (spec). The residues option (default false) promotes any specified atoms to whole residues. The polymer option restricts the result to only the biopolymer chains with the same sequences as the chains in chain-spec (the same macromolecular entities). Example:

select #2 polymer #1/a
– select biopolymer chains in model 2 that have the same sequence as chain A of model 1

The minimumLength and maximumLength filters apply only to pseudobonds.

Modify Selection

Usage: selectadd | subtract | intersect )  spec  [ residues  true | false ]
Usage: selectup | down | clear )
Usage: ~select  spec  [ residues  true | false ]

Subcommands of select can be used to:

The ~select command can be used to deselect specified items (like select subtract) or with a blank specification to deselect everything (like select clear).

Zone Selection

Usage: select zone  ref-spec  cutoff  [ other-spec ] [ extend  true | false ] [ residues  true | false ]

The command select zone selects atoms and/or surfaces in other-spec that are within the cutoff distance of the atoms and/or surfaces in ref-spec. A blank (omitted) other-spec indicates “all.” Although molecular surfaces can be included in the reference items (ref-spec), their membership in the resulting zone is not evaluated directly because their selection is tied to that of the corresponding atoms. The extend option (default false) indicates whether the reference items should also be selected. The residues option (default false) indicates whether to select all atoms of a residue if any atom in the residue is within the zone. See also: surface zone, volume zone, zone


select zone ligand 4.5 protein res t
sel zone #1.2 8
sel zone sel 5 extend t

Alternatively, the top-level select command can be used with zone specifications to give the same results as the examples above:

select ligand :<4.5 & protein
sel #1.2 @<8 & ~ #1.2
sel sel @<5

One advantage of select zone, however, is that it works with non-atomic model types.

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