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 atomic coordinates opened in Chimera becomes a model with an associated model ID number. Surfaces and other types of models also have ID numbers. Some tools in Chimera create models that are hidden from the Model Panel, however.

A molecular structure file may contain multiple sets of coordinates for the same set of atoms. In PDB files, these coordinate sets are delimited with MODEL and ENDMDL records. Appending a submodel number to the primary model number allows uniquely specifying atoms despite multiple occurrences of the “same” atom (same atom name, residue name, and residue number) in the file. Submodel numbers are assigned sequentially starting with 1 (#0.1, #0.2, etc.). Multiple orbitals in a Gaussian cube file are also loaded as submodels.

The term “models” will be used to indicate submodels and/or models that are not subdivided into submodels because they are operationally the same: each can be handled independently of the others and listed separately in the Model Panel. At first, the submodels in a model may be collapsed into a single row (for example, model #3 in the figure below), but the listing can be expanded to the individual submodels using the group/ungroup function.

The figure shows columns:

• model 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 a single line.

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. Just the favorites or all functions can be listed, using the setting below the list. Functions can be added to or removed from the favorites by showing all functions and using the Fav checkboxes. The Configure... button allows customizing which columns appear in the left side of the panel and which functions are applied to double-clicked models.

Functions:

• 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 hydrogens... add hydrogens to the chosen model(s); equivalent to using AddH
• add/edit note... add a text description for the model (the Model Panel can be configured to show these descriptions in a Note column; see also session notes)
• attributes... list model attributes and allow changes
• biological unit - add copies to generate the biological unit according to BIOMT matrices in the input file; full atomic copies are generated for N-mers of N ≤ 6, whereas for N-mers of N ≥ 7, the copies are generated as low-resolution surfaces from Multiscale Models. Not all structures include BIOMT matrices. See also: fetching PDB-biounit (biological assembly) and PQS files
• 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 - focus the view on the chosen model(s) and set the center of rotation method to center of view (as if using the command focus on those models)
• group/ungroup - collapse multiple chosen entries into a group with a specified name, or expand a single chosen entry that is already a group into its contents; grouping is hierarchical (groups may contain other groups)
• 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
• rainbow... color the chosen model(s) over a range with the Rainbow tool (see also the command rainbow)
• Ramachandran plot... show the distribution of peptide φ,ψ angles (a Ramachandran plot) for each chosen model that contains protein; also implemented as the command ramachandran
• rename... change the name of each chosen model and/or group. The name is initially based on input filename or assigned by Chimera when creating the model (for multi-Mol2 files, see also the New Molecules preferences). Another way to change the model name attribute is with the command setattr.
• render attribute... open the Render/Select by Attribute tool to depict (with color, etc.) or select atoms, residues, and molecule models by their attribute values
• save sphgen (available when a sphere file has been opened) - save spheres or atoms as a sphere file in the sphgen format used by DOCK
• select - select the chosen model(s) for subsequent operations or commands
• select chain(s)... select subsequently specified chains in the chosen model(s). The chains are identified in two ways, by ID and by covalent connectivity, and the listing by ID includes chain descriptions from the PDB, if available. Any combination of chains from the two identification methods can be chosen for selection.
• 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
• UniProt info... start PDB/UniProt Info to retrieve UniProt annotations and map them to sequence
• write PDB - save models as PDB files

The Configure... button brings up another panel with three sections for customizing the Model Panel:

• The Buttons section was used in older versions of Chimera to classify functions as frequently or infrequently used. Currently Chimera uses a favorites list instead, where just favorites or all functions can be shown in the Model Panel. To configure which functions are favorites, change from showing just favorites to showing all in the Model Panel, then use the Fav checkboxes.

• 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-added descriptive text for the model; 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.

Model Panel customization settings are stored in a user's preferences file.