Toolbars provide quick mechanism to perform various commands. In general, they operate on the selected structures as appropriate. There are currently 6 toolbars:

• Home: this toolbar contains a set of the most common actions. In the future, users will be able to add their favorite action to this toolbar
• Molecule Display: provides a set of actions to change the display of a molecular structure and perform some structural analysis (e.g. show hydrogen bonds).
• Nucleotides: supports changing the display of nucleotide elements within a structure.
• Graphics: changes various graphics values such as the background, lighting type, camera modes, etc.
• Map: controls for manipulating map (volume) data
• Right Mouse: settings for operation of the right mouse. Allows the right mouse to be used for a large number of purposes including movement of structures, manipulation of maps and structures, and annotations.

Currently, most actions are performed using commands entered on the ChimeraX Command Line Interface. To get a list of the available commands, enter usage into the command line. To get more information about a command enter help command and ChimeraX's web browser will be displayed with the documentation for that command. Some of the most commonly used commands are described in the next slides, but the first it's important to know how ChimeraX refers to models, chains, residues, and atoms.

Target specification

Basic commands

delete:

deletes the specified atoms, bonds, or pseudobonds. Note: this is not undoable!

open, close, save:

The open command reads data in several input formats (e.g PDB/mmCIF, DICOM, Gromacs, MRC, and many others) from local files, urls, and online databases. This command is also used to read ChimeraX session files (.cxs). The close command removes models from ChimeraX, including any submodels. The save command saves the current session or map. It is also used to save images from the current display.

select:

A selection specifies items (models or their parts) for subsequent operations; the selected items are highlighted with green outlines in the graphics window. The select command can:

• make a new selection of specified items
• modify an existing selection
• select by zone (distance cutoff from specified items)

show,hide (disp,~disp):

The commands show and hide display and undisplay the specified atoms, bonds, pseudobonds, cartoons, molecular surfaces, and entire models. Following the usual convention, a blank specification means “all.” Both commands take an optional target argument that limits the effect to atoms (a), bonds (b), pseudobonds (p), cartoons (c), surfaces(s) or entire models (m).

undo,redo:

The undo and redo commands provide a limited undo/redo capability. At this point, only show, hide, color, size, style, cartoon, and select are supported. In some cases there are restrictions on even those commands. We expect this to be extended in the future.

view:

The view commands changes the window focus to the specied items or "all".

Depiction commands

cartoon (ribbon):

The cartoon or ribbon command shows a simplified backbone representation of the specified biopolymer residues. The cartoon style subcommand provides several options for the style of the representation, including width, thickness, and shape.

nucleotides

The nucleotides command generates special representations of nucleic acids, with choices for mode: atoms, fill, ladder, stubs, tube/slab, slab

style:

The style command sets atom/bond display styles and the number of dashes per pseudobond. The style can be one of the following: sphere, stick, or ball. The style command also provides options for ring fill as well as pseudobond dashes.

surface:

The surface command creates and displays molecular surfaces, either atomically detailed solvent-excluded surfaces (default) or lower-resolution Gaussian surfaces. Surface display style (solid, mesh, or dot) can be adjusted with surface style. There are several options that support how the surface is created, including the atoms enclosed by the surface and the atoms incuded in the surface.

color:

Depending on the type of coloring, color may apply to atomic models and their parts, including cartoon and molecular surface representations, and volume data (map) displays. Subcommands include color sequential (rainbow) to support rainbow coloring of atomic models, color modify to adjust the color for atomic models, color byattribute to color based on an atom, residue, or model attribute, and coloring by map values: color sample, color electrostatic, and color gradient. There are also subcommands to color surfaces by distance (color radial, color cylindrical, color height and to color by zone (color zone).

Analysis commands

hbonds:

The hbonds command uses atom types and geometric criteria to identify hydrogen bonds (H-bonds) involving the specified atoms.

matchmaker (mmaker):

The matchmaker (or mmaker) command superimposes protein or nucleic acid structures by first creating a pairwise sequence alignment, then fitting the aligned residue pairs.

morph:

The morph command creates a trajectory that morphs between two or more atomic models. The trajectory can be played back with the coordset command or the slider graphical interface.

Useful tools

• Log
• Echoes commands that have been executed, with any truncations expanded
• Shows messages and other output information, potentially including hyperlinks and command-execution links
• Context menu and log command provide support for:
  • Saving the log to an HTML file
  • Adding a thumbmnail image to the log
  • Adding metadata associated with a model to the log
  • Setting whether echoed commands should link to documentation or be execution links

Useful tools

• Log
• Model Panel
• Shows model hierarchy of currently open models
• Allows selective display of models
• Can show/hide models or submodels

Useful tools

• Log
• Model Panel
• Side View
• Helps locate model in Z direction
• Provides access to hither-and-yon clipping planes

Useful tools

• Log
• Model Panel
• Side View
• Sequence Viewer
• Displays sequence of currently loaded structures
• Selection linked to structure
• Can display alignments
• Alignment headers can show conservation (AL2CO) as well as consensus

Useful tools

• Log
• Model Panel
• Side View
• Sequence
• Basic actions
• Quick access to:
  • select named sets of atoms
  • show/hide or color atoms
  • show/hide or color cartoon segments
  • show/hide or color molecular surface patches

The ChimeraX toolshed provides a mechanism for other developers to add new tools and commands to ChimeraX. Several additional tools are already available on the toolshed, so users should check there for new content. Also, the UCSF team will release updates to individual ChimeraX components by publishing them to the toolshed.

• Scripting is executing a set of commands from a file
• Useful for repetitive tasks
• Can serve as documentation
• ChimeraX commands may be read in from a file or typed directly in the command line interface
• The ChimeraX browser combines scripting with simple HTML to create web interactions with ChimeraX. To use, simply add command links (e.g. "<a href="cxcmd:open 1hgg">open 1hgg</a>") in your html and open the file using ChimeraX's web browser.

• The best, most up-to-date source for help is the user's guide. It is available directly from the ChimeraX help menu (Help→User Guide) or on the web https://www.rbvi.ucsf.edu/chimerax/docs/user/.
• You can also subscribe to the e-mail list: ChimeraX-users, which is regularly monitored by the ChimeraX team.