The Model Panel Model Panel icon

The Model Panel lists the models in Chimera and conveniently enables many operations upon them. There are several ways to start the Model Panel, a tool in the General Controls category.

Each file of atomic coordinates opened in Chimera becomes a model with an associated model ID number. Surfaces and other types of models also have ID numbers. Some tools in Chimera create models that are hidden from the Model Panel, however.

A molecular structure file may contain multiple sets of coordinates for the same set of atoms. In PDB files, these coordinate sets are delimited with MODEL and ENDMDL records. Appending a submodel number to the primary model number allows uniquely specifying atoms despite multiple occurrences of the “same” atom (same atom name, residue name, and residue number) in the file. Submodel numbers are assigned sequentially starting with 1 (#0.1, #0.2, etc.). Multiple orbitals in a Gaussian cube file are also loaded as submodels.

The term “models” will be used to indicate submodels and/or models that are not subdivided into submodels because they are operationally the same: each can be handled independently of the others and listed separately in the Model Panel. At first, the submodels in a model may be collapsed into a single row (for example, model #3 in the figure below), but the listing can be expanded to the individual submodels using the group/ungroup function.

Model Panel

The figure shows columns:

Individual models or multiple models can be chosen with the left mouse button. A block of models can be chosen by dragging, or by clicking on the first (or last) line in the desired block and then Shift-clicking on its last (or first) line. Ctrl-click toggles the state (chosen or not) of a single line.

Once one or more models have been chosen within the left side of the Model Panel, any of several functions represented by buttons on the right side of the panel can be executed. Just the favorites or all functions can be listed, using the setting below the list. Functions can be added to or removed from the favorites by showing all functions and using the Fav checkboxes. The Configure... button allows customizing which columns appear in the left side of the panel and which functions are applied to double-clicked models.


Close dismisses the Model Panel. Help opens this manual page in a browser window.

Model Panel Configuration

The Configure... button brings up another panel with three sections for customizing the Model Panel:

Model Panel customization settings are stored in a user's preferences file.

UCSF Computer Graphics Laboratory / May 2022