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 can be treated as a separate model. Thus, "models" will be used to indicate submodels and/or models that are not subdivided into submodels.

Nonmolecular models are also given ID numbers. A molecule model can share a number with one or more molecular surface models and/or objects (any of the other model types).

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 category.
Model Panel
In the figure, models 0.2 and 1 have been chosen. Color swatches show the model-level color of each molecule model (when the model is not chosen). Individual models or blocks of models can be chosen with the left mouse button. Ctrl-click adds to an existing choice rather than replacing it. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

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 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 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.

  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: Show model color behind model name places a panel of the model-level color behind the model name. The color of a model when opened is its model-level color.
  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.