The Model Panel

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.

The figure shows the default columns:

• ID number
• model color (a color well)
• whether Active (movable)
• whether Shown (display-enabled)
• Name (model name)

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:

• activate - activate for motion; the opposite of deactivate
• activate all - activate all models even if not chosen in the left side of the panel (the previous pattern of activities is saved and can be restored using the button's alternate function, restore activities)
• activate only - activate the chosen model(s) and deactivate all the others
• add/edit note... add arbitrary text that can be shown as a Note column (see configuration)
• add hydrogens... add hydrogens to the chosen model(s); equivalent to using AddH
• attributes... list model attributes and allow changes
• clipping... open the Per-Model Clipping tool
• close - close (remove) the model(s)
• color by SS... color peptides/proteins by secondary structure with the Color Secondary Structure tool
• compute SS - define the secondary structure of peptides/proteins in the chosen model(s) using ksdssp with the specified parameter values. Hitting return (Enter) or clicking OK runs the calculation and dismisses the dialog, while clicking Apply runs the calculation without dismissing the dialog. Clicking Save as Defaults saves the parameter settings in the preferences file; subsequently, those settings will be used with the ksdssp algorithm when peptide/protein structures that lack secondary structure assignments are read in, when MatchMaker is used with the Compute secondary structure assignments option, or when compute SS is specifically invoked.
• copy/combine... combine multiple molecule models into a single model or make a copy of a single molecule model (see also the command combine). The new model will be assigned the specified ID number and its name will appear in the Model Panel and other model lists. A coordinate system (reference model) must be specified. The reference model's untransformed coordinates (if part of the combination) and current transformation will be carried over into the new model. The coordinates of any other model in the combination will be transformed relative to the reference model. To ensure that residues in the new model will be uniquely specifiable, it is necessary to allow either renaming chains (changing chain IDs) or renumbering residues when the input models contain more than one chain with the same ID. The original or source model(s) can be closed. Clicking OK generates the new model and dismisses the dialog, while clicking Apply generates the new model without dismissing the dialog. Changes in chain identifiers or residue numbering are reported in the Reply Log.
• deactivate - deactivate for motion; the opposite of activate
• focus - center the display on the chosen model(s)
• hide - disable display of the chosen model(s) (see display hierarchy); the opposite of show
• match... open the MatchMaker tool to superimpose structures with similar sequences and folds; at least two molecule models must be chosen for this operation to be available
• minimize... energy-minimize the chosen molecule model(s), first adding hydrogens and assigning parameters as needed (see the command minimize)
• rainbow... color the chosen model(s) over a range with the Rainbow tool (see also the command rainbow)
• rename... change model name (initially based on input filename or assigned by Chimera when creating the model; for multi-Mol2 files, see also the New Molecules preferences)
• render/sel by attr... open the Render/Select by Attribute tool to depict (with color, etc.) or select atoms, residues, and molecule models by their attribute values
• select - select the chosen model(s) for subsequent operations or commands
• select chain(s)... select subsequently specified chains in the chosen model(s)
• sequence... show chain sequences (start the Sequence tool)
• show - enable display of the chosen model(s) (see display hierarchy); the opposite of hide
• show all atoms - show the chosen model(s) and display all atoms within them
• show only - show the chosen model(s) and hide all of the others
• surface main - for the chosen model(s), display the molecular surface of any atoms categorized as main
• tile... open Tile Structures to arrange the (two or more) chosen models in a plane
• toggle active - toggle the status of each chosen model between activated and deactivated for motion (make the status of each its current opposite)
• trace backbones - in each chosen model, display only a simplified trace for bonded chains containing amino acid or nucleic acid residues, consisting of real backbone bonds (-[N-CA-C]_n- in peptides and -[O5'-C5'-C4'-C3'-O3'-P]_n- in nucleic acids)
• trace chains - in each chosen model, display only a simplified trace for bonded chains containing amino acid or nucleic acid residues, consisting of one atom per residue (connect the CA atoms in peptides, C4' atoms in nucleic acids)
• transform as... transform each (initially) chosen model using the rotation/translation matrix of the single model chosen when the dialog's OK button is clicked
• write PDB - bring up a dialog for saving models as PDB files

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.

• 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.

• The Columns section determines which model attributes will be shown in the left side of the Model Panel. The descriptions below are in the order in which the columns would be shown, from left to right.
  • ID - model (and submodel, if applicable) number
  • [color] - for each molecule model, a color well showing the model-level color; blank for molecular surface models and other model types. Clicking a color well opens the Color Editor and allows the color to be changed.
  • Active - whether the model is activated for motion; see activate and deactivate
  • Shown - whether the model is shown; see hide and show
  • Name - model name; see rename
  • Note - user-created text annotation; see add/edit note
  • Input file - for local files, a pathname (relative if the file is in a subdirectory of the working directory, otherwise full); for files fetched from databases, an identifier or filename for that database entry
  Show model color behind model name shows the model-level color of each molecule model in the Name column, with the text of the name when the model is chosen, otherwise with a swatch of color behind the name.

• 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.