The select command has been enhanced in Chimera and now has dual functions:
The older function, indicated by the all keyword or a model_number(s) argument, is to select a model or models for subsequent move, rock, roll and turn commands as well as interactive mouse manipulations. In Chimera, this type of selection is more often called activation and should not be confused with the selection used to specify atoms for subsequent operations (which is the newer function; see below). 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. The model_number(s) argument should be expressed as one or more model numbers or ranges of model numbers separated by commas, not preceded by #. The activation status of models can also be controlled in the Model Panel or by toggling the boxes under the Command Line.
The newer function, indicated by an atom-spec argument or the keyword up or down, is selection, as used in Chimera to specify atoms for subsequent operations. Lack of any argument is interpreted as specification of all atoms. 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. Using the keyword up (down) broadens (narrows) an existing selection, like pressing the up (down) arrow key. Examples:
select #1- select model 1 (including all of its atoms, bonds, and residues)
select 1,5-8- activate models 1 and 5 through 8 for motion
~select :/isHelix- deselect any atoms in amino acid residues in helices