The Model Panel Model Panel icon

Each file of coordinates opened in Chimera becomes a model with an associated model ID number. Some PDB files are further subdivided into multiple structures designated with MODEL and ENDMDL records; thus, the concept of submodels was created to allow unique atom specifications even when multiple structures in the same file contain identical residue and atom names. Submodel numbers are assigned sequentially starting with 1 when the input file contains more than one set of MODEL and ENDMDL records (#0.1, #0.2, etc.); the numbers in the file are not used. Each submodel is treated as a separate model. Thus, "models" will be used to indicate submodels, models that are not subdivided into submodels, or a combination of the two. Surfaces and other nonmolecular objects are also assigned model ID numbers. Molecules, surfaces, and objects can share a number.

The Model Panel shows the current models and conveniently enables many operations upon them. There are several ways to start the Model Panel, a tool in the Inspectors and Utilities categories.
Model Panel
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.

Individual models or blocks of models can be chosen (highlighted) with the left mouse button. Ctrl-click adds to an existing choice rather than replacing it. To highlight a block of models without having to hold down the mouse button, click on the first (or last) and then Shift-click on the last (or first) in the desired block. In the figure, model 1 and submodel 2 of model 0 have been chosen.

Configure... allows customization of which settings are shown as checkboxes on the left side of the panel, which functions are considered frequently used, and what functions are applied to double-clicked models. Close dismisses the Model Panel. Help brings up the Model Panel 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.

  1. The Buttons section shows all the functions that can be listed on the right side of the Model Panel. If a checkbox is activated, the adjacent function will be included in the frequently used list; the remaining functions are included in the infrequently used list. The frequently used/infrequently used toggle button is below the function list on the right side of the Model Panel.
  2. The Columns section determines which model attributes will be shown in the left side of the Model Panel:
  3. The Double Click section controls which functions will be executed upon a model when the model is double-clicked in the left side of the Model Panel. The default is attributes...; however, there can be zero or many functions in the list for execution. Clicking an entry in the Function menu on the right causes it to appear in the Execution list on the left. Clicking an entry in the Execution list removes it from that list. The functions will be executed in the order listed.