The Model Panel

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 General Controls category. 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:

• 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
• attributes... list model attributes and allow changes
• BLAST on PDB - BLAST the sequence of a single model against sequences in the PDB using the NCBI BLAST program blastcl3 (Network BLAST, see BLAST Basic Overview). This will only work for proteins, and the button will only appear for users able to run blastcl3 from the system command line (with arguments but no preceding path). The E-value and matrix used can be adjusted. Results are converted to a multiple sequence alignment and displayed using Multalign Viewer.
• 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 HELIX and SHEET records are read in, when MatchMaker is used with the Compute secondary structure assignments option, or when compute SS is specifically invoked.
• 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; 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)
• render by attr... open the Render by Attribute tool to depict atoms, residues and models by their attribute values (with color, etc.)
• select - select the chosen model(s) for subsequent operations or commands
• select by attr... open the Select by Attribute tool to select by attribute values
• select chain(s)... select subsequently specified chains in the chosen model(s)
• sequence... open the sequence panel showing chain sequences
• 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 ligand - display the molecular surface of atoms in the chosen model(s) determined to be in the ligand category, if any; equivalent to the command surface ligand
• surface main - display the molecular surface of atoms in the chosen model(s) determined to be in the main category; equivalent to the command surface main
• tile - "tile" the chosen models as described for EnsembleTile; at least two models must be chosen for this operation to be available
• 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.

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:
   • Active - whether the model is activated for motion; see activate and deactivate
   • ID - model (and submodel, if applicable) number
   • Input file - pathname, relative if the file is in a subdirectory of the working directory, otherwise a full pathname; if the file was opened using a 4-character PDB identifier, only the PDB identifier is shown
   • Name - filename
   • Shown - whether the model is shown; see hide and show
   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.