The ChimeraX Menu

Although most functionality is currently in commands, the ChimeraX menu includes basic file operations and undo, choices for selection, and access to several tools. See also: the ChimeraX window, context menus, Basic Actions, the Command Line

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

• Open... a subset of open command functionality
• Fetch by ID... show the Fetch by ID graphical interface to fetch data from online sources
• Open DICOM Folder... open all files of the specified format (currently DICOM only) in the specified directory and its subdirectories
• Save... a subset of save command functionality
• Set Working Folder... specify the current folder or location for input/output when no path is specified. Upon startup with the ChimeraX icon, the initial working folder is ~/ (user's home directory) on Linux and ~/Desktop on Windows and Mac. Startup from the system command line uses the current shell directory instead. See also: cd, pwd
• Close Session – same as the command close session

• Undo
• Redo

• Chains – chains in currently open structures
• Chemistry
  • Element – elements by atomic symbol
  • IDATM Type – atom type
  • Functional Group
  • Protein – amino acids, peptides, and proteins
  • Nucleic Acid – nucleosides, nucleotides, RNA, and DNA
• Residues – residues in currently open structures, sorted into nonstandard residues, standard nucleic acids, and standard amino acids
• Structure
  • Backbone – biopolymer backbone atoms: peptide N, CA, C, O, nucleic acid phosphoribosyl backbone, and any directly attached hydrogens
  • Ions – ions
  • Ligand – ligand
  • Main – main
  • Secondary Structure – protein/peptide secondary structure
    • Coil – amino acid residues not in helix or strand
    • Helix – amino acid residues in helices
    • Strand – amino acid residues in strands
  • Sidechain + Connector – amino acid sidechain + CA (for connectivity to cartoon), nucleic acid base + ribose, and any directly attached hydrogens
  • Sidechain Only – amino acid sidechain, nucleic acid base, and any directly attached hydrogens
  • Solvent – solvent
• Sequence... find and select a specified amino acid or nucleotide sequence or sequence pattern
• Zone... select atoms or residues within (<) and/or beyond (>) a specified distance from the currently selected atoms. There is also an option to deselect current selection, which affects the results when selecting within only. If both the within and beyond options are checked, both criteria must be met; for example, the atoms or residues must fall within 12 Å of but farther away than 8 Å from the current selection. OK performs the selection and closes the dialog, whereas Apply performs the selection without closing the dialog. See also: select zone, zone atom specification
• By Attribute Value... show Render/Select by Attribute set to its Select tab
• Contacts... use Select Contacts to select atomic or chain-chain contacts based on specified criteria (details...)
• Clear – deselect any existing selection
• Invert
  • Selected Models – within model(s) that contain a selection, select items that are currently unselected and deselect items that are currently selected
  • All Models – select all items that are currently unselected and deselect all items that are currently selected
• All – select all models and their parts
• 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
• Menu Mode: mode (applies only to selecting with the Select menu and Basic Actions tool)
  • Replace (initial default mode)
  • Add (+)
  • Subtract (–)
  • Intersect (∩)
• User-Defined Selectors
  • [any selectors previously defined with the name command or Define Selector, see below]
• Define Selector... name and save the current selection or (re)define a selector with a target specification string

The Actions menu applies to the displayed models only (those with    checkboxes in the Model Panel checked for themselves and any parents). Within those models, it works on the current selection, or if none, all applicable items.

• Atoms/Bonds – show/hide
  • Show
  • Show Only
  • Hide
  • Atom Style – atom/bond style settings
    • Stick
    • Ball & Stick
    • Sphere
    • Ring Fill
      • Thick
      • Thin
      • None

  The following apply to biopolymers (peptides and nucleic acids):

  • Show Side Chain/Base – show amino acid sidechain + CA (for connectivity to cartoons), nucleic acid base + ribose
  • Backbone Only – hide cartoon and show atoms in peptide backbone, nucleic acid phosphoribosyl backbone
  • Chain Trace Only – hide cartoon and show chain-trace atoms: amino acid CA, nucleic acid P
  • Nucleotide Style – nucleotides settings
    • Ladder
    • Stubs
    • Slab Base, Ribose Tube
    • Slab Base, Ribose Atoms
    • Atoms (Filled Rings)
    • Atoms (No Ring Fill)
    
    
  • Delete – delete atoms/bonds (caution: irreversible)
  
  
• Cartoon – cartoon segments can be shown/hidden for individual residues in a biopolymer chain; showing cartoon hides backbone atoms unless their simultaneous display has been enabled with cartoon suppress false
  • Show
  • Hide
  The cartoon style settings apply to whole models, except that edge shape can be set differently for nucleic and for protein helix, strand, and coil:
  • Rounded Edges – oval cross-section (for a round cross-section, use cartoon style to set width = thickness, for example: cartoon style sel width 1.5 thick 1.5)
  • Squared Edges – rectangular cross-section
  • Piped Edges – barbell cross-section
  • Tube Helices – protein α-helices as curved cylinders
  
  
• Surface – show/hide molecular surfaces, adjust style and transparency of molecular and/or volume surfaces
  • Show
  • Hide
  • Solid
  • Mesh
  • Dot
  • Transparency – can be set differently for atomic patches within a single molecular surface, whereas the styles above apply to entire models only
    • 0%
    • 10%
    • 20%
    • 30%
    • 40%
    • 50%
    • 60%
    • 70%
    • 80%
    • 90%
    • 100%

• Color – see also color
  • [20 of the commonly used named 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
  • Custom... use the system color picker
  • All Options... open the Color Actions dialog for access to all built-in named colors and finer control over which types of items are colored (for example, background only or cartoons only)
  
  
• Label – see also label
  • Atoms
    • Name
    • Element
    • IDATM Type – by atom type
    • Custom Text – arbitrary text and/or values of attributes, as described for the text option of label. Examples:
      • hello world
      • {0.bfactor:g}
    • Other – various specific atom attributes
    • Off
  • Residues
    • Name – for example, TRP
    • Specifier – chain ID and residue number (/A:183)
    • Name and Number – residue name and number (TRP 183)
    • Chain, Name, Number – chain ID, residue name, and number (/A TRP 183)
    • 1-Letter Code – 1-letter code for standard amino acid and nucleic acid residues (e.g., W), full name for other residues (e.g., HOH)
    • Code and Number – as above plus residue number (W 183)
    • Chain, Code, Number – chain ID, 1-letter code, and residue number (/A W 183)
    • Custom Text – arbitrary text and/or values of attributes, as described for the text option of label. Examples:
      • wild type
      • {0.chain_id}
      • {0.phi:.1f},{0.psi:.1f}
    • Other – various specific residue attributes
    • Off
  • Set Label Height
• Focus – see also view
• Set Pivot – see also cofr
• Inspect – show the Selection Inspector to view/modify attributes of the current selection

• Cartoons/Nucleotides
  • Ribbons/Slabs – cartoon style initial defaults + nucleotide bases as rectangular boxes
  • Cylinders/Stubs – cartoon style protein α-helix cylinders + nucleotide stubs (half-rungs)
  • Licorice/Ovals – cartoon style without 2°-structure detail + nucleotide bases as ellipsoids
• Custom – user-defined presets
• Initial Styles – based on automatic styling
  • Original Look – initial appearance from automatic styling, which depends on the number of chains in an atomic structure (however, settings such as silhouettes and cartoon style may be different if they were changed since the structure was opened)
  • Sticks – all atoms as sticks, simple lighting, etc. (as for automatic styling of structures with 0 chains)
  • Cartoon – cartoon plus atomic detail near residues classified as ligand and ions, simple lighting, etc. (as for automatic styling of structures with 1-4 chains)
  • Space-Filling (Chain Colors) – all atoms as spheres except sticks for ligand and balls for solvent, chain colors, shadows, etc. (as for automatic styling of structures with 5-249 chains)
  • Space-Filling (Single Color) – all atoms as spheres, ambient-only lighting, etc. (as for automatic styling of structures with ≥250 chains)
• Molecular Surfaces – molecular surfaces with different coloring options:
  • Atomic Coloring (Transparent) – same color(s) as the underlying atoms, 70% transparent
  • Chain ID Coloring (Opaque) – chain colors, opaque
  • Ghostly White – white, 80% transparent
• Overall Look
  • Publication 1 (silhouettes) – silhouettes on, depth-cueing off, background color white
  • Publication 2 (depth-cued) – depth-cueing on, silhouettes off, background color white
  • Interactive – depth-cueing on, silhouettes off, background color default (user preference)

A top-level Volume menu containing the tools in the Volume Data category can be shown from the Tools menu (Tools... Volume Data... Show Volume Menu) and subsequently hidden with its own entry: Hide Volume Menu

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