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, including 3D data and 2D annotations (2D labels and color key), any sequence data, and certain data-associated tools and results panels (plots, etc.). It also restores several global settings to their startup values: camera mode, lighting and depth-cueing, clipping, surface capping, and graphics settings such as background color and silhouettes.
See also: open, hide, delete, quit, Model Panel, ChimeraX sessions, the ChimeraX menu