Menu Listing

The major menu headings are File, Select, Actions, Controllers, Settings, Extensions, and Help. Unavailable menu options are shown in a lighter color.

File

Open... bring up the Chimera Open File Dialog
Open Session... bring up a dialog for opening a previously saved session (Python file)
Save Session - save the current session as session.py in the working directory (uses SimpleSession)
Save Session As... bring up a dialog for saving the current session to a specified name and directory location (uses SimpleSession)
Close Session - clear session contents without exiting from Chimera
Save Image... open the Image Panel for saving a TIFF file
Quit - exit from Chimera

Select

Chemistry
- amino acid category
  (note that the existing amino acid categories can be changed and new categories defined and listed here, using the extension ResProp)
- chemical group
- element
- IDATM type
- residue type (residue name; only those found in currently open structures will be listed)
Draw Mode
Structure
- backbone (only applies to amino acids and/or nucleic acids)
  - full - the amide backbone in peptides, the sugar-phosphate backbone in nucleic acids
  - minimal - a continuous series of bonded atoms connecting the chain trace atoms (-[N-CA-C]_n- in peptides and -[O5'-C5'-C4'-C3'-O3'-P]_n- in nucleic acids)
- ions - ions, using the same definition as surface calculations
- ligand - ligand, using the same definition as surface calculations
- main - main, using the same definition as surface calculations
- secondary structure (only applies to peptides/proteins)
  - helix - residues in helices as defined by PDB HELIX records in the input file, or if these are not present, using ksdssp
  - sheet - residues in strands as defined by PDB SHEET records in the input file, or if these are not present, using ksdssp
  - turn - residues in turns as defined by PDB TURN records in the input file
- side chain/base (only applies to amino acids and/or nucleic acids)
  - with CA/C1'
  - without CA/C1'
- solvent - solvent, using the same definition as surface calculations

(note that other categorizations can be defined and listed here, using the Selector Construction Panel; see Construct Selector... below)

Clear Selection - clear (deselect) the current selection
Midas Atom Specifier... use atom specification syntax for selection
Sequence... select by amino acid or nucleotide sequence
Zone... select atoms and bonds within (or beyond) a specified distance from the currently selected atoms, on a per-atom or whole-residue basis
Selection Mode (current_mode) - control whether a new selection via the menu will be added to, subtracted from, intersected with, or used to replace the existing selection
Select All - select all open models and their constituent parts
Save Selection... name and save the current selection
Undo - undo the most recent selection operation
Saved Selections - retrieve a previously saved selection
Construct Selector... open the Selector Construction Panel to define a complex selection of atoms and bonds

Other means of selection include picking from the graphics window and using the select buttons within the Model Panel and Pseudobond Panel.

Actions

Actions are applied to items that have been selected. When nothing is selected, the various operations (Color, Display, Label, Represent, and Surface) act on everything at the level specified by the Target setting. This menu listing is fairly concise, but a more detailed explanation is available.

Inspect - open the Selection Inspector, which lists what items are selected, shows their properties, and allows their properties to be changed
Target (current_target) - control whether actions should apply only to the selected atoms/bonds or to the entire residues and models containing them; possible values of current_target are:
- selected atoms/bonds
- selected residues
- selected models
- unselected atoms/bonds
- unselected residues
- unselected models
Realm (current_realm) - only applies when the Target is unselected atoms/bonds or unselected residues; possible values of current_realm are:
- selected models - only act on unselected parts of models containing selections
- all models - act on unselected parts of models containing selections and on models not containing any selections
Color
- [20 top tier colors]
- by element - use a built-in color-by-element scheme
- from editor - use the current Color Editor color
- none - remove color assignments
- applies to - whereas Target controls how widespread the change will be, this setting controls which level(s) in the coloring hierarchy will be affected; a more detailed explanation is available.
  - default
  - residues only
  - atoms/bonds only
  - surfaces only
  - labels only
  - atom labels only
  - bond labels only
- all colors - a further menu of all 60 built-in colors
Display
- on
- off
- backbone only
- side chain/base only
- chain trace only
Label
- clear - undisplay atom labels
- name - label atoms by name
- element - label atoms by element
- IDATM type - label atoms by atom type
- other... label atoms with other atom-associated information
- residue
  - clear - undisplay residue labels
  - name - label residues by name
  - number - label residues by sequence number (including the chain ID, if any)
  - both - label residues by name and sequence number
Represent - type of representation
- wire (wireframe)
- stick
- ball & stick
- sphere (CPK)
- ribbon - type of secondary structure ribbon shown (see also resrepr). Ribbons are only drawn for proteins and nucleic acids. Protein secondary structure is determined from HELIX and SHEET records in the input file, or if these are not present, using ksdssp.
  - none
  - flat
  - edged
  - round
- surface - type of surface representation (always acts on entire surfaces)
  - solid
  - mesh
  - dot
- line width - pixel thickness of lines drawn to show bonds in the wireframe representation (always acts on entire models)
  - 1
  - 2
  - 3
  - 4
  - 5
Surface
- clear - undisplay the surface
- main - display the surface for atoms classified as main
- ligand - display the surface for atoms classified as ligand
- style - type of surface representation (always acts on entire surfaces)
  - solid
  - mesh
  - dot

Controllers

The Controllers act upon specific models and objects open in Chimera.

Midas Emulator - show/hide the Midas Emulator command line
Side View - open the Side View for easy adjustment of scale and clipping planes
Model Panel - open the Model Panel, which lists the current models and enables many operations upon them
Pseudobond Panel - open the Pseudobond Panel, which lists the current pseudobond groups and enables many operations upon them
Distances - open the distance measurement panel
Angles/Torsions - open the angle measurement panel (not implemented; for now, use the command angle)
Adjust Torsions - open the rotatable bonds panel

Settings

The Settings affect the Chimera environment rather than directly affecting specific models or objects.

Camera - adjust the Camera viewing parameters, such as whether perspective is used
Color - open the Color Editor to define new colors
Effects - adjust the Effects viewing parameters, which affect depth cueing
Lenses - open the Lens Inspector to define lenses (regions of alternative types of display)
Reply Log - open the Reply Log, which contains informational, warning, and error messages from Chimera
Rotation - adjust the Rotation viewing parameters, such as center of rotation
2D Texture - open the 2D Texture Editor to map colors to properties or property ranges
Preferences - show and change Preferences settings

Extensions

Manager - open the Extension Manager to list all extensions and control their startup status
In general, there will also be several submenus of the form
Extension Category
- Start - launch all extensions in the category (listed below)
- Extension1
- Extension2
where choosing an individual extension launches it.

See the Extensions section of the Chimera User's Guide for descriptions of individual extensions.

Help

Selection of Help menu items opens a browser window containing the requested information.

About Help - describe help features in Chimera
Context Help - describe the feature that is clicked next
User's Guide - open the Chimera User's Guide
Version Info - show what version of Chimera is being used
Software Updates - report whether the version of Chimera being used is older than the latest version available on the web (requires internet connectivity)
Feedback - show e-mail addresses for reporting Chimera problems or making suggestions
Citing Chimera - show how to cite usage of Chimera
Registration... - open the form for registration as a Chimera user