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 coordinates opened in Chimera becomes a model with an associated model ID number. Surfaces and other types of models also have ID numbers.

Some files contain multiple structures or multiple sets of coordinates for the same structure. In PDB files, these multiple structures are delimited with MODEL and ENDMDL records. Appending a submodel number to the primary model number allows atoms to be specified uniquely even when multiple structures in the same file contain identical residue and atom names. Submodel numbers are assigned sequentially starting with 1 (#0.1, #0.2, etc.).

The term "models" will be used to indicate submodels and/or models not subdivided into submodels because they are operationally the same: each is a separate entry in the Model Panel and can be handled independently of the others.

Model Panel

The figure shows the default columns:

Which columns are shown can be customized.

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 single line. In the figure, models 1 and 3.2 are chosen.

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. Each function is classified as frequently used or infrequently used; the toggle button below the list controls which set is listed.

Configure... allows customization of what is included in the left side of the panel, which functions are considered frequently used, and which functions are applied to double-clicked models. Close dismisses the Model Panel. Help opens this manual page in a browser window.

The functions are:

Model Panel Configuration

The Configure... button brings up another panel with three sections for customizing the Model Panel. The three sections are organized like index cards with their names on tabs across the top: Buttons, Columns, and Double Click. Clicking on a tab brings the corresponding card to the front.

UCSF Computer Graphics Laboratory / November 2009