Choosing Settings... Preferences from the menu opens the Preferences Tool. Options within are grouped by Category:

• Background
• General
• Image Credits
• Messages
• Midas
• Mouse
• New Molecules
• PDB
• Page Setup
• Preferences

Save saves the current Preferences Tool settings to the preferences file. Restore replaces the current settings with those already specified in the file, whereas Reset replaces the current settings with the defaults. Help opens this manual page in a browser window. Close dismisses the Preferences Tool.

Default settings are indicated below in bold.

The Background section of the Preferences Tool includes:

• Background color (a color well) - the color is reported as "No" if the background color has not been changed, indicating that the default (black) is being used
• Selection highlight method (outline/fill) - how a selection is highlighted in the graphics window
• Selection highlight color (a color well, green by default) - what color to use for highlighting a selection in the graphics window
• Draw lens borders (true/false) - whether to draw outlines of any lenses in the graphics window
• Lens border color (a color well, green by default) - what color to use for outlining any lenses in the graphics window

The General section of the Preferences Tool includes:

• Confirm exit (true/false) - whether to ask for confirmation after Session... Exit has been chosen from the menu
• Show balloon help (true/false) - whether to show balloon help, explanatory text that pops up when the cursor is left in certain positions
• Show atomspec balloon (true/false) - whether to show label information when the cursor is left on top of an atom or bond.
• Atomspec display style (simple/Midas atomspec/Midas-dependent) - whether to describe atoms with a simple style that consists of residue name, residue number, and atom name, or with a Midas atomspec string; the default is to use the simple style when the Midas Emulator is not shown and atomspec strings when the Midas Emulator is shown (affects atomspec balloons and the Structure Measurements panels)
• File lists path style (file - leading path/full path) - how to list files and their locations in certain dialogs (such as Files to read at startup within the Midas section of the Preferences Tool); a change will not be evident until after Chimera is restarted
• Confirm starting extension (true/false) - whether to ask for confirmation before starting certain extensions (for example, MainChain or AddH)
• Toolbar visible (no/yes/auto) - whether or not to display the tool bar, where icons for extensions are placed; the auto option only shows the tool bar if it contains one or more icons
• Toolbar side (left/right/top/bottom) - position of the tool bar relative to the graphics window
• Use short open/save browser (true/false) - whether open/save dialogs should show only the two lowest directory levels (more details)
• Open dialog starts in directory from last session (true/false) - whether the first open/save dialog invoked during a session should start in the directory where a file was last opened or saved in the previous session, or in the current working directory. The default is true on Windows systems, false on the others.

The Image Credits section of the Preferences Tool specifies information to be included in saved TIFF image files. This information does not affect the image itself.

• Artist (user's login name by default) - optional, name of the image creator
• Copyright (blank by default) - optional, a copyright statement

The Messages section of the Preferences Tool controls the disposition of command, status, warning, and error messages.

• Show replies at startup (true/false) - whether to open the Reply Log upon Chimera startup
• Show status line (true/false) - whether to show a line for status messages under the main Chimera window (otherwise, status messages are not visible); can also be set from the Accelerators dialog
• Clear status line after (5 seconds/10 seconds/20 seconds/30 seconds/1 minute/never) - how long a status message will be shown in the status line (when not overwritten by subsequent status messages); applies to status messages appearing in certain dialogs as well as the main Chimera status line
• Command (reply log only/dialog) - whether command messages should appear in the reply log only, or also generate a dialog box
• Warning (reply log only/dialog) - whether warnings should appear in the reply log only, or also generate a dialog box
• Error (reply log only/dialog) - whether error messages should appear in the reply log only, or also generate a dialog box

The Midas section of the Preferences Tool is only available when the Midas Emulator is shown.

Files to read at startup refers to what files, if any, contain commands to be executed when (or if) the Midas Emulator is shown. There are two defaults:

• $HOME/.chimera/midasrc (in a directory named .chimera in the user's home directory, here referred to as $HOME)
• .chmidasrc in the current directory

The midasrc mechanism is similar to that in MidasPlus, where a file named .midasrc in the user's home directory was automatically executed upon program startup. In general, the same file can be used here after commands unsupported by Chimera have been removed.

A midasrc-type file can be created by manual text-editing or by using Record... in the Command History tool to save commands already used in Chimera.

By default, structures are rotated with the left mouse button and XY-translated with the middle mouse button (for more details, see mouse manipulation).

Mouse button functions can be reassigned within the Mouse section of the Preferences Tool. This panel may be used to assign functions to the left, middle, and right mouse buttons (Buttons 1, 2, and 3, respectively). Ctrl-1, Ctrl-2, and Ctrl-3 indicate the functions of the left, middle, and right mouse buttons when the Ctrl key is also held down. Current assignments are indicated by color-highlighted checkboxes. Since a button can only have one function, selecting a function by mouseclick turns off the previously selected function in that row. The figure shows the default assignments. Going from left to right, the symbols across the top of the panel signify rotation, XY-translation, Z-translation, scaling, atom and bond picking (selection), lens control, and a pop-up menu bar when the standard menu bar is not visible (not implemented).

Continue rotation after mousing (true/false) indicates whether to rotate continuously when the mouse button assigned to rotation is released while the cursor is in motion.

The New Molecules section of the Preferences Tool controls how newly opened molecules will initially appear:

• use new color for each model (true/false) - set the model-level color (see coloring hierarchy) differently for each new molecule model; submodels with the same main model number will be assigned the same model-level color. This preference can also be controlled with the commands set/~set autocolor.
• otherwise, use color (a color well, by default showing a light gray color) - color at the model level, see coloring hierarchy
• ribbon depiction (none/flat ribbon/edged ribbon/rounded ribbon) - type of secondary structure ribbon shown (see also resrepr). Ribbons are only drawn for proteins and nucleic acids. Protein secondary structure is determined from HELIX and SHEET records in the input file, or if these are not present, using ksdssp.
• line width (1 by default) - pixel width of lines drawn to show bonds in the wire draw mode
• atom style (dot/ball/endcap/sphere) - atom draw mode
• bond style (wire/stick) - bond draw mode
• stick diameter (0.2 by default) - angstrom thickness of bonds in the stick draw mode
• ball size (0.25 by default) - fraction of VDW radius used for ball radius when atoms are in the ball draw mode
• coloring by element (true/false) - whether byatom coloring is used; this overrules the model-level color above, see coloring hierarchy
• auto-chaining (off/on) - whether to connect atoms that precede and follow undisplayed segments (whether to draw pseudobonds between them)

The PDB section of the Preferences Tool includes:

• Fetch from web as necessary (true/false) - whether to retrieve an input PDB file from the Protein DataBank web site when it is not found locally
• Personal PDB directories - additional directories to look in for PDB files; the user may Add a directory to the list of places to look, or choose a previously added directory from the list and then Delete it from the list

The Page Setup section of the Preferences Tool sets specifications for images saved to TIFF files using the Image Panel. This section can also be invoked from the Image Panel.

• Units (centimeters/inches/millimeters/points) - the units used for describing the options below
• Printer Resolution - values in this section should be compatible with the specifications of the printer used
  • Horiz. dots per unit (by default, 400 per inch or the equivalent in other units)
  • Vert. dots per unit (by default, 400 per inch or the equivalent in other units)
  • Colors per dot (3/3+black/4/5/5+black/6)
  • Shades per color (2 by default)

The Preferences section of the Preferences Tool specifies:

Location - where the preferences file for the current session should be located:

• preferences (in the current directory)
• .chimera/preferences (in a directory named .chimera in the current directory
• $HOME/.chimera/preferences (in a directory named .chimera in the user's home directory, here referred to as $HOME)