Chimera Menus

The major menu headings are:

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

• Open... bring up the Chimera 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 (uses SimpleSession; 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 (uses SimpleSession)
• Close Session - clear session contents without exiting from Chimera

• Save Image... open the Image Panel for saving an image file
• Save PDB... bring up a dialog for saving models as PDB files

• Quit - exit from Chimera

• Chain
  (only chain IDs found in currently open structures will be listed)
• Chemistry
  • element
  • functional group
  • IDATM type
• Residue
  • amino acid category
    (note that the existing amino acid categories can be changed and new categories defined and listed here, using ResProp)
  • name
    (only residue names found in currently open structures will be listed)
• 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 HELIX records in the input PDB file or by ksdssp
    • strand - residues in strands as defined by SHEET records in the input PDB file or by ksdssp
    • turn - residues in turns as defined by TURN records in the input PDB 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
• 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

• Save Selection... name and save the current selection
• Saved Selections - retrieve a previously saved selection
• Construct Selector... open the Selector Construction Panel to define a complex selection of atoms and bonds

Actions menu operations relating to molecular surfaces apply only when the selection contains the corresponding molecule models or parts of molecule models (or nothing), regardless of whether a molecular surface model is itself selected.

• 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/bond labels
    • atom labels (includes residue labels)
    • bond labels (does not include pseudobond labels; a bond label can be created/deleted by picking a bond and using the Selection Inspector)
    • all of the above (default)
    • background
    • depth cue - set the color used to indicate depth
  • by element - use a built-in color-by-element scheme; does not affect ribbons
  • from editor - use the current Color Editor color
  • 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
  • off - undisplay atom labels
  • name - label atoms by name
  • element - label atoms by element
  • IDATM type - label atoms by atom type
  • other... label atoms with an arbitrary string or with other atom-associated information:
    • 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)
  • residue - Residue labels are placed next to a "representative" atom: CA in amino acid residues, C4' in nucleic acid residues, and in other residue types, the atom with the name that falls first in alphabetical order.
    • 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 atoms, bonds, and/or ribbon segments that are displayed (possibly including items that are invisible). If any items are selected, only those both selected and displayed are considered. Focusing consists of:
  1. adjusting the view to include item(s) both selected and displayed (similar to the command window)
  2. making the center of the bounding box of the item(s) the center of rotation (like the command cofr)
• Atoms/Bonds
  • show
  • hide
    
  • backbone only - only applies to residues in bonded chains containing amino acid or nucleic acid moieties; includes 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 containing amino acid or nucleic acid moieties. 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
  • chain trace only - only applies to residues in bonded chains containing amino acid or nucleic acid moieties; a chain trace consists of one atom per residue, CA in each amino acid and C4' in each nucleic acid residue. Choosing this turns auto-chaining on.
  • wire width - always affects entire molecule models even though the selection may be narrower
    • 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 - delete atoms/bonds (caution; irreversible except by reopening the original input)
• Ribbon - secondary structure ribbon (see also the commands ribbon and ribrepr). Ribbons are only drawn for proteins and nucleic acids. Protein secondary structure is determined from HELIX and SHEET records in the input PDB file or by using ksdssp.
  • show
  • hide
  • flat
  • edged
  • round
    (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). The surface representation options (solid, mesh, and dot) are always applied to entire models even though the selection 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 by tcolor, rainbow, or the rainbow function in the Model Panel will not become transparent.
    • 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)

• 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... bring up a dialog for saving specifications as a parsable text file. 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.

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

• 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

• Check for 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

• Citation Info - show how to cite usage of Chimera
• Registration... open the form for registration as a Chimera user
• About UCSF Chimera - report the version of Chimera being used and show copyright information