Chimera Menus

The major menu headings are:

• File
• Select
• Actions
• Presets
• Tools
• Favorites
• Help

• 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)
• 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)
• Save Session As... bring up a dialog for saving the current session to a specified name and directory location

• 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 without exiting from Chimera
• Quit - exit from Chimera

• 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
  • 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)
    • helix - residues in helices
    • strand - residues in strands
    • turn - residues in turns according to 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

• 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

• 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
• Undo - undo the most recent selection operation

• Name Selection... name and save the current selection (see also the command namesel). The selection contents are remembered, not the process by which the selection was generated (i.e., if all oxygens in the current structure(s) are selected, later retrieving the named selection when different structures are open will not select their oxygens).
• Named Selections - retrieve a previously saved selection
• Construct Selector... open the Selector Construction Panel to define a complex selection of atoms and bonds

• 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
  • wire width - always affects entire molecule models even though the targets may be narrower (like the command linewidth)
    • 1
    • 1.5
    • 2
    • 2.5
    • 3
    • 4
    • 5
  • wire (wire representation)
  • stick (stick representation)
  • ball & stick (ball-and-stick representation)
  • sphere (sphere or CPK representation)
  • 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 surface (see also the commands surface and surfrepr). Surface actions apply only when the targets include portions of the corresponding molecule models (or nothing is selected), regardless of whether the molecular surface models are themselves selected. The surface representation options (solid, mesh, and dot) always apply to entire molecular surface models even though the targets may be narrower.
  • show
  • hide
  • solid
  • mesh
  • dot
  • transparency - atom-level surface transparency (distinct from the transparency/opacity included in the definition of an atom-level surface color). 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 the command color)
  • [20 top tier colors]
    Whereas Target controls how widespread a change will be, the following settings control which level(s) in the coloring hierarchy will be affected by a subsequent color choice.
    • atoms/bonds
    • ribbons
    • surfaces (atom-level surface colors; see coloring hierarchy)
    • atom labels
    • bond labels (does not include pseudobond labels; a bond label can be created/deleted by picking a bond and using the Selection Inspector)
    • residue labels
    • all of the above (default)
    • background - set the background color (regardless of the current targets)
    • depth cue - set the color used for front-to-back shading (depth cueing) (regardless of the current targets)
  • by heteroatom - use a built-in color-by-element scheme, except leaving carbon atoms unchanged; does not affect ribbons, residue labels, background, or depth cue colors
  • by element - use a built-in color-by-element scheme; does not affect ribbons, residue labels, background, or depth cue colors
  • 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 colors - a further menu of all 60 built-in colors
• Label (see also the command label)
  • 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
    • defaultRadius - default VDW radius
    • occupancy - occupancy value, if any
    • radius - VDW radius (may have been changed by the user from the default VDW radius)
    • serialNumber - serial number in the input file
    • surfaceCategory - category to which the atom has been assigned automatically or manually using msms cat (or surfcat)
      (newly generated numerical, boolean, or string-valued atom attributes will also be listed)
  • residue (see also the command rlabel) - A residue label is placed at the centroid of the displayed atoms in the residue. When ribbon is displayed instead of mainchain atoms, mainchain atom positions are still used in computing the centroid.
    • 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-associated information
• Focus - focus the view on the target atoms, bonds, and/or ribbon segments that are also displayed, possibly including items that are invisible (like the command focus). Focusing consists of:
  1. adjusting the view to include the item(s) (similar to window)
  2. setting the center of rotation to the center of view (like cofr view)
• Set Pivot - set the center of rotation to the center of the bounding box of the targets (like the command cofr). When nothing is selected, Set Pivot restores the default center of rotation method, center of models, in which the center of rotation is the center of the bounding box of the currently active models (displayed portions only; may include items that are invisible).

• Target - control whether actions should apply to only the selected atoms/bonds or to the entire residues, chains, or models containing them (or the complement of any of these):
  • selected atoms/bonds
  • selected residues
  • selected chains
  • selected models
  • unselected atoms/bonds
  • unselected residues
  • unselected chains
  • unselected models
  • realm (current_realm) - only applies when the Target is unselected atoms/bonds, unselected residues, or unselected chains; 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

• 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 specifications can be written in the simple (e.g., #0 PHE 16 CD1) or command-line specifier (e.g., #0:16@CD1) naming style. 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

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 (see also the command preset). Presets are provided for a handful of usage scenarios; of course, many more combinations of settings are possible.

• Interactive presets are meant for interactive manipulation and analysis. They may change what items (atoms, ribbons, surfaces) are displayed and how they are colored. The ribbons setup shows atomic detail for all nucleic acid residues, and for any amino acid sidechains and other residues within 3.5 Å of a ligand residue or metal ion. A 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. Surfaces of nonpeptides (which do not have Kyte-Doolittle hydrophobicity values) will be colored to match the underlying atoms instead.
  
  
• Publication presets are intended for generating images for presentation and publication. They do not change what items are displayed or their colors, but may change their styles and the color of the background. For example, choosing a preset with rounded ribbon or licorice will not turn on ribbon display, but will adjust any currently displayed ribbon segments; similarly, only the currently displayed atoms and bonds will be shown as sticks. Publication presets may decrease interactive performance because finer divisions are used to depict curved objects (molecular surfaces, ribbons, etc.). Individual display parameters are discussed in more detail in the tips on preparing images.

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

• Category
  • Tool1
  • Tool2

If certain tools or extensions have been started and not quit during a Chimera session, their instances will appear in the bottom section of the Tools menu:

• 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

The Favorites menu contains the Preferences in addition to any subset of 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

• 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
• 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 - report whether the version of Chimera being used is older than the latest version available on the Web (requires internet connectivity)
• 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)