Chimera Commands Index

The select command has been enhanced in Chimera and now has dual functions. The newer function is selection. The older function is activation for motion.


select atom-spec

~select atom-spec

select [ up | down | invert | invert sel ]

The newer function of select is selection of atoms and/or surface models. The atom-spec can specify any combination of atoms and surfaces; a blank specification selects all. The effect of “select atom-spec” on an existing selection depends on the selection mode. ~Select removes the specified atoms from the selection regardless of selection mode.

Keyword arguments:

select  #1
- select all atoms and bonds in model 1
~select  :/isHelix
- deselect any atoms in amino acid residues in helices

See also the keyboard shortcuts rn, rp, ri for shifting a selection to the next residue in a chain, the previous residue, and to include intervening residues, respectively. These can be used as commands with ac (for example: ac rn). See also: namesel, zonesel, arrow key shortcuts

Activation for Motion

select [ all | model_number(s) ]

~select [ all | model_number(s) ]

The original function of select is indicated by use of the keyword all or the absence of a pound sign # before model_number(s). This function, now usually called activation, is to control whether a model can be manipulated interactively. Activation/deactivation allows manually moving one model relative to another. The activation status of models can also be controlled using the Model Panel or checkboxes under the Command Line.

The model_number(s) argument should be one or more model numbers or ranges separated by commas, not preceded by #. The keyword all indicates that all models should be activated. ~Select all will then revert to the previous activation state. This feature is convenient for switching back and forth between moving models relative to one another and global motion of all models.


select  1,5-8
- activate models 1 and 5 through 8 for motion

See also: split, movie-related commands