The major menu headings are:

• File
• Select
• Actions
• Presets
• Volume (not always present)
• Tools
• Favorites
• Aliases (not always present)
• Help

← File

• Open... bring up the Open File dialog
• Fetch by ID... specify by database identifier a file to be retrieved and opened

• Restore Session... bring up a dialog for opening a previously saved session (Python file); clicking the filename of a session shows its associated thumbnail image and session notes, if any
• Save Session - save the current session in the working directory; available when the current session has been named with Save Session As... or was started by restoring an existing session; does not update the associated thumbnail image, if any
• Save Session As... bring up a dialog for saving the current session to a specified name and location; allows including session notes and/or a thumbnail image of the current Chimera display

• Save Image... bring up the Save Image dialog
• Save PDB... bring up a dialog for saving PDB files
• Save Mol2... bring up a dialog for saving Mol2 files
• Export Scene... bring up a dialog for exporting the scene from Chimera

• Close Session - clear session contents, show the Rapid Access interface
• Quit - exit from Chimera

← Select

• Chain
  [only chain IDs found in currently open structures will be listed]
• Chemistry
  • element
    [many entries]
  • functional group
    [many entries]
  • IDATM type
    [many entries]
• Residue
  • amino acid category
    [many entries]
    (the existing amino acid categories can be changed and new categories defined and listed here, using ResProp)
  [only residue names found in currently open structures will be listed, sorted into nonstandard residues, standard nucleic acids, and standard amino acids]
• 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
  • markers - markers and links (such as from Volume Tracer)
  • nucleic acid - nucleosides, nucleotides, RNA, and DNA
  • protein - amino acids, peptides, and proteins
  • secondary structure (only applies to peptides/proteins; helix and strand assignments are taken from the input structure file or generated with ksdssp)
    • coil - amino acid residues not in helices or strands
    • helix - amino acid residues in helices
    • strand - amino acid residues in strands
  • 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

• Sequence... find and select a specified amino acid and/or nucleotide sequence (atoms and bonds in any/all matching segments will be selected)
• Atom Specifier... use atom specification syntax for selection
• By Attribute Value... open the Select by Attribute tool to select by attribute values
• Zone... select atoms and bonds within (or beyond) a specified distance from the currently selected atoms, on a per-atom or whole-residue basis. If both the within and beyond options are checked, only the atoms that fit both criteria will be selected, for example, those within 12 Å but farther away than 8 Å.

• Clear Selection - clear (deselect) the current selection
• Invert (all models) - select all currently unselected atoms and deselect all currently selected atoms
• Invert (selected models) - in models containing selections only, select all currently unselected atoms and deselect all currently selected atoms
• Select All - select all open models and their constituent parts
• 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
  • append
  • intersect
  • replace (default)
  • subtract
  • Show (Hide) mode icon - show, or hide if already shown, an icon in the status line for the current menu selection mode: A for append, I for intersect, R for replace, or S for subtract; clicking the icon cycles through the modes
• Broaden - expand the current selection up a level in the selection cascade
• Narrow - narrow a previously broadened selection down a level in the selection cascade
• Undo - undo the most recent selection operation

• Name Selection... name and save the current selection (see also the command namesel and the Rapid Access interface). Named selections can be restored using the Select menu (see Named Selections below) or the Rapid Access interface, and their names can be used for command-line atom specification.
• Named Selections - retrieve a previously saved selection

← Actions

• When nothing is selected, the action affects all applicable items: molecule models and/or surface models, depending on the action.
• Surface actions apply not only to selected surface pieces, but also to the molecular surface patches of selected atoms.

• Atoms/Bonds (see also the commands display and represent)
  • show
  • show only
  • hide
    
  • backbone only - only applies to residues in bonded chains of amino acids or nucleic acids
    • chain trace - show only one atom per residue, CA in each amino acid and C4' in each nucleic acid residue (turns on auto-chaining)
    • full - show only the amide backbone in peptides, the sugar-phosphate backbone in nucleic acids
    • minimal - show only 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)
  • side chain/base - only applies to residues in bonded chains of amino acids or nucleic acids. Each amino acid side chain includes any side chain atoms from CB outward, plus the atom CA (for connectivity purposes); similarly, each nucleic acid base includes the base plus the sugar atom to which it is bonded, usually named C1'.
    • show - display side chains/bases and turn auto-chaining on
    • show only - undisplay other atoms in the chain and turn auto-chaining off
  • stick (stick representation)
  • ball & stick (ball-and-stick representation)
  • sphere (sphere or CPK representation)
  • wire (wire representation)
  • wire width (see also the command linewidth) - always affects entire molecule models even though the targets may be narrower
    • 1
    • 1.5
    • 2
    • 2.5
    • 3
    • 4
    • 5
  • rings (see also the commands fillring and aromatic) - aromatic rings can only be shown as filled when their aromaticity display is turned off, and the aromaticity settings always affect entire models even though the targets may be narrower
    • fill thick
    • fill thin
    • fill off
    • aromatic disk
    • aromatic circle
    • aromatic off
  • nucleotide objects (see also the command nucleotides)
    • off - show atoms instead of sugar/base abstractions, remove any nucleotide ring fill
    • settings... open the Nucleotides tool for controlling special nucleotide representations
  • delete - remove atoms/bonds (caution: irreversible) like the command delete
• Ribbon - secondary structure ribbon (see also the commands ribbon and ribrepr). Ribbons are only drawn for proteins and nucleic acids. By default, showing ribbon hides the corresponding mainchain atoms (but see ribbackbone). Protein helix and strand assignments are taken from the input structure file or generated with ksdssp.
  • show
  • hide
  • flat
  • edged
  • rounded
  • supersmooth
    (note that additional styles can be defined and listed here, using the Ribbon Style Editor)
• Surface - molecular surfaces and surface models. Even though the targets may be narrower, representations (solid, mesh, and dot) always apply to entire surface pieces.
  • show
  • hide
  • solid
  • mesh
  • dot
  • transparency (surfaces colored with tcolor will not be affected)
    • 0%
    • 10%
    • 20%
    • 30%
    • 40%
    • 50%
    • 60%
    • 70%
    • 80%
    • 90%
    • 100%
    • other... set surface transparency percentage to a typed-in value
    • base color - use transparencies included in color definitions (rather than overriding them via this menu)
• Color (see also color, scolor)
  • [top 20 colors]
  • by heteroatom - use a built-in color-by-element scheme, except leaving carbon atoms unchanged
  • by element - use a built-in color-by-element scheme
  • from editor - open the Color Editor and use its current color; apply any color adjustments made in the Color Editor until it is closed or reassigned to a different coloring operation by clicking a color well. If during that time the selection is changed, any color adjustments will be applied to the new selection.
  • none - remove color assignments; assignments at other levels in the coloring hierarchy may become visible
  • all options... open the Color Actions dialog for access to all 60 colors and finer control over which types of items are colored (for example, background only or ribbons only)
• Label (see also the commands label and rlabel for details, including label positioning, and labelopt for custom labeling)
  • off - undisplay atom labels
  • name - label atoms by name (with any alternate location ID appended)
  • element - label atoms by element
  • IDATM type - label atoms by atom type
  • other... label atoms with an arbitrary string or with the values of atom attributes:
    • altLoc - alternate location identifier, if any
    • bfactor - B-factor value, if any
      (etc.)
    Newly generated numerical, boolean, or string-valued atom attributes will also be listed.
  • residue
    • off - undisplay residue labels
    • name - label residues by name
    • 1-letter code - label standard amino acid residues by one-letter code, other residues by name
    • specifier - label residues by specifier (residue number, insertion code, and chain ID); see custom residue labeling for number alone
    • name + specifier - label residues by name and specifier
    • 1-letter code + specifier - label standard amino acid residues by 1-letter code and specifier, other residues by name and specifier
    • custom... custom-label residues with an arbitrary string and/or other residue information such as attributes
  • options... open the Labels preferences for setting options such as font size
• Focus - focus the view on the targets that are also displayed and set the center of rotation method to center of view (analogous to the command focus); if nothing is selected, set the center of rotation method to front center; an exception to the preceding is that the center of rotation method is not changed if it is independent
• Set Pivot - set the center of rotation to the center of the bounding sphere of the targets and set the center of rotation method to fixed (analogous to the command cofr); if nothing is selected, set the center of rotation method to front center. See also: Mouse preferences, Set Pivot in the atom context menu

• Inspect - open the Selection Inspector, which lists what items are selected, shows their attributes, and allows their attributes to be changed
• Write List... bring up a dialog for saving specifications as a parsable list. Specifications can be saved for the selected (or unselected) atoms, bonds, pseudobonds, residues, molecules (molecule models), or models (non-molecule models: molecular surface, surface, VRML, and volume). The naming style controls the format of the specifications. Clicking the Log button sends the information to the Reply Log instead of saving a file.
• Write PDB... bring up a dialog for saving the selection as a PDB file

← Presets

A preset is a predefined combination of display settings. Choosing an entry in the Presets menu applies its settings and is much easier than adjusting the many settings individually. Presets are provided for a handful of usage scenarios; of course, many more combinations of settings are possible. See also: the preset command, the New Molecules preferences

• Custom presets are user-defined, see below
  
  
• Interactive presets are meant for interactive manipulation and analysis. They may change which items (atoms, ribbons, surfaces) are displayed and how they are colored. The background color is set to black and the ribbon path method to B-spline.
  • Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short. Nucleic acids may be shown with special sugar and base representations (as produced by Nucleotides), with the level of abstraction dependent on size.
  • Interactive 2 (all atoms) - displays all atoms and bonds as wires, with heteroatoms colored by element. Carbons are shown in the model colors so that models will be distinguishable from one another.
  • Interactive 3 (hydrophobicity surface) - shows amino acid hydrophobicity in the Kyte-Doolittle scale with colors ranging from dodger blue for the most hydrophilic to white at 0.0 to to orange red for the most hydrophobic (different color-codings can be applied with rangecolor or Render by Attribute). Surfaces of nonpeptides will be colored to match the underlying atoms instead.
  
  
• Publication presets are intended for generating images for presentation and publication. They do not change which items are displayed or their colors, but may change the styles of the items. For example, ribbons are not hidden/shown, but any existing ribbon will be adjusted to rounded ribbon or licorice according to the chosen preset. Similarly, atoms and bonds are not hidden/shown, but any wire will be changed to sticks. The background color is set to white. Publication presets may decrease interactive performance because they increase smoothness by using finer divisions to depict curved objects (ribbons, molecular surfaces, etc.). Individual display parameters are discussed in more detail in the tips on preparing images.
  • Publication 1 (silhouette, rounded ribbon)
  • Publication 2 (silhouette, licorice)
  • Publication 3 (depth-cued, rounded ribbon)
  • Publication 4 (depth-cued, licorice)
  • Publication 5 (flat ribbon) with both silhouettes and depth-cueing, and ribbon inside color set to white
  
  
• Add Custom Presets... open the Presets preferences for specifying directories in which to look for custom preset scripts

← Volume

The Volume menu is a replica of the Tools... Volume Data menu. It can be shown/hidden using Tools... Volume Data... Volume Menu on Menubar or the similar entry in the Tools menu of Volume Viewer.

← Tools

The Tools menu contains the Chimera tools or extensions. In general, there will be several submenus of the form

• Category
  • Tool1
  • Tool2

There are also entries related to third-party extensions (plugins available separately from the Chimera download):

• Additional Tools
  • Insilichem/Tangram - Tangram is a collection of molecular modelling tools for UCSF Chimera developed by the InsiliChem group, Universitat Autònoma de Barcelona
  • More Chimera plugins... Chimera plugins on the web, a nonexhaustive list
  • Add third-party plugin location... open the Tools preferences to allow specifying the locations of (separately downloaded) third-party plugins, so that Chimera can find them and add any corresponding menu entries or icons
  • Create your own plugin/extension... Chimera Programmer's Guide examples

• Tool_name (or Tool_name - data)
  • Raise - open the tool interface (if closed) and bring it to the front
  • Hide - close the tool interface without exiting
  • Quit - exit from this instance of the tool

← Favorites

The Favorites menu contains the Preferences in addition to any subset of the entries in the Tools menu (individually specified using the Tools preferences). The default contents are

• Model Panel - open the Model Panel, which lists the current models and enables many operations upon them
• Side View - open the Side View for easy adjustment of scale and clipping planes
• Command Line - show the Command Line
• Reply Log - open the Reply Log containing informational, warning, and error messages from Chimera

• Add to Favorites/Toolbar... open the Tools preferences
• Preferences... show and allow changes in Preferences settings

← Aliases

Start-of-line aliases defined with the command alias will be listed here. Choosing an entry from the Aliases menu executes the alias. The Aliases menu will only be present when there is at least one start-of-line alias.

← Help

Documentation pages requested from the Help menu will be shown in a browser window.

• Search Documentation... bring up a dialog for searching the local (bundled) Chimera documentation (which includes the User's Guide, Programmer's Guide, and other items listed in the Chimera documentation index)

  One or more terms can be entered in the search field. Combinations of terms can be indicated with and, or, not and parentheses. Separating terms with a space is equivalent to using and. Pressing return (Enter) or clicking Search initiates the search. Hits will be listed in the Search Results column as links to the corresponding documentation.

• User's Guide - open the Chimera User's Guide
• Commands Index - open the Chimera Commands Index
• Tutorials - open the Tutorials section of the Chimera User's Guide
• Context Help - describe the feature that is clicked next (avoid clicking the top bar of a dialog, since that will fail to bring up a help page)

• Check for Updates (requires internet connectivity) - see if any production releases are newer than the version in use, and if so, provide links to download them
• Contact Us - show e-mail addresses for asking questions or making suggestions
• Report a Bug... open a form for bug submission
• Citation Info - show how to cite usage of Chimera
• Registration... open a form for registration as a Chimera user
• About UCSF Chimera - report what version of Chimera is being used and show copyright information (like the command version)