Tool: Model Panel

In ChimeraX, models include atomic structures, molecular surfaces, pseudobond models, volume data, marker sets, and graphical objects, for example, those read from BILD format. A model can be read from a file, derived from another model, or created from scratch. Model ID numbers can be assigned automatically or specified by the user.

Models are arranged hierarchically into groups. For example, an NMR ensemble open as model #1 could contain different coordinate sets as submodels #1.1, #1.2, ... #1.10. Hiding #1 hides all of its submodels, regardless of their individual hide/show settings (details...). A submodel is a model in its own right, and the general term “model” may refer to a model at any level of the hierarchy. Models that are grouped automatically include:

• NMR ensembles of atomic models
• multiple contour surfaces of the same volume data

Like other tools, the Model Panel can be opened from the Tools menu (more...). It lists the current models, with columns:

• Name – model name; doubleclick to edit
• ID – model number; doubleclick to edit
• a color well; click to change the color interactively
• – show/hide checkbox
• – selection checkbox (a checkbox containing “–” means that the model is partially selected)
• Skip (if enabled as described below) – exclude model from next/previous actions

Disclosure triangles allow collapsing/expanding the hierarchy when multiple levels are present. Model names and/or ID numbers (and thus groupings) can be changed by double-clicking and entering a new value, or by using the the rename command. See also: Toolbar, info

One or more entries (rows) can be highlighted with the mouse. Buttons on the right act on only the highlighted entries, or if none are highlighted, all entries:

• Close – close model(s)
• Hide – hide model(s); see also next/previous
• Show – show model(s); see also next/previous
• View – focus the view on model(s) and turn off clipping
• Info – for atomic structures, show model information in the Log; for DICOM data, show the DICOM Browser (if patient or study model) or DICOM Metadata (if series model)
• Next (if enabled as described below; down arrow is the keyboard shortcut)
• Previous (if enabled as described below; up arrow is the keyboard shortcut)

The corresponding commands are shown in the Log.

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Adding Next/Previous Buttons

The Model Panel context menu includes an option to Show Sequential Display Controls. Checking this option will add Next and Previous action buttons for rapidly flipping the display through the list of models (showing each model in turn while hiding others), as well as a Skip column to allow excluding a model from these actions. When these controls are shown and the mouse focus is in the Model Panel, next/previous actions can also be performed with the down/up arrow keys. The setting to show these controls is automatically saved as a preference for future sessions.