The command close removes the specified model(s) from ChimeraX, including any submodels at lower levels of the hierarchy. For example, close #3 will close any models #3.N, #3.N.N, etc. As per the usual convention, a blank specification indicates all models.
The command close session closes all models plus various tool and results panels (plots, sequence alignments, etc.) and 2D labels.
See also: open, hide, delete, quit