Hi David,
If generating separate maps based on a distance cutoff from the atoms is acceptable, you could try using Color Zone (Tools… Volume Data… Color Zone).
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http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
First you’d have to color the components different colors, then select all their atoms. In Color Zone, use the slider to pick a suitable cutoff (if any) and then click “Split Map” to get separate maps for the zones.
If the components are all separate models, you could color them uniquely and then select them with commands such as:
rainbow models
select
Alternatively, although the Segment Map tool (in same menu as Color Zone) uses the watershed method and not the atoms, you could try Segment Map and then interactively group/ungroup the resulting segments to correspond with your docked components. I don’t
know how easy or hard that might be.