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

• Background
• Collaboratory
• General
• Image Credits
• Image Setup
• Messages
• Midas
• Mouse
• New Molecules
• PDB
• Preferences
• Tools
• Web Access

For just the category being shown: Reset replaces the current settings with the original defaults, Restore replaces the current settings with those previously saved in the preferences file, and Save saves the current settings to the preferences file. Equivalent operations can be performed for all categories at once within the Preferences section of the Preferences Tool.

Help opens this manual page in a browser window, and 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, No Color by default) - when set to no color, the background is black
• Label font (Sans Serif/Serif/Fixed) (Normal/Bold/Italic/Bold Italic) (6/8/9/10/11/12/16/18/24/30/36)
• 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 Collaboratory section of the Preferences Tool controls some aspects of the Collaboratory extension. Setting a port number and publishing the IP address may help enable use under certain problematic network conditions.

• Logging (not yet implemented)
  • Collaboratory logging enabled (true/false) - whether to save Collaboratory messages in a log file
  • Collaboratory log location - pathname for the log file
• IP address
  • Publish IP enabled (true/false) - whether to override the IP address supplied by the computer with the address specified below; needed when a computer supplies a "local" IP address rather than the address needed for internet communications
  • IP address to publish - the IP address of the computer or router supplying the internet connection
• Port number
  • Publish port enabled (true/false) - whether to designate a specific network port number for communications (otherwise, the port will be randomly allocated by CORBA)
  • Port to publish - the port number (must be greater than 1024, as ports up to 1024 are reserved for use by the system)

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/command-line specifier/command-line-dependent) - whether to describe atoms with a simple style that consists of residue name, residue number, and atom name, or with an atom specification string (affects atomspec balloons and the Structure Measurements panels); the default is to use atom specification strings when the Command Line is shown and the simple style when the Command Line is not shown
• 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
• Toolbar visible (no/yes/auto) - whether or not to display the toolbar, where icons are placed; the auto option only shows the toolbar if it contains one or more icons
• Toolbar side (left/right/top/bottom) - position of the toolbar 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 image files (TIFF, PNG). 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 Image Setup section of the Preferences Tool sets specifications for images saved to 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
• Image Resolution
  • Pixels per unit (by default, 100 per inch or the equivalent in other units) - the desired resolution; multiplied by the image width and height in the Image Panel to yield the dimensions in pixels
  • Resolution Calculator - suggests a resolution that minimizes output file size for printing purposes by computing the optimal number of printer pixels required to represent one screen pixel
    • Printer dots per unit (300 by default)
    • Colors per dot (3/3+black/4/5/5+black/6)
    • Shades per color (2 by default)
• Antialiasing - used to decrease jaggedness along straight edges within saved images (does not affect the interactive display)
  • Supersample (1x1/2x2/3x3/4x4/5x5/6x6) - how many pixels are sampled in the X and Y dimensions for each pixel in the final saved image; higher values increase smoothness and calculation time

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

• 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 Command Line (Midas Emulator) is shown.

Files to read at startup refers to what command files, if any, should be executed when the Command Line is started. 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.

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 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 display (off/on) - whether to show a secondary structure ribbon; 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.
• ribbon cross section (edged/flat/round/any additional styles created and named with the Ribbon Style Editor) - style of secondary structure ribbon shown (see also ribrepr)
• ribbon scaling (Chimera default/any additional scalings created and named with the Ribbon Style Editor) - secondary-structure-specific scaling of ribbon height and width
• ribbon hides backbone atoms (true/false) - whether showing ribbon for residues within the model hides backbone atoms for those residues (see the command ribbackbone for details)
• line width (1.0 by default) - pixel width of lines depicting bonds (when in the wire draw mode)
• atom style (dot/ball/endcap/sphere) - atom draw mode
• bond style (wire/stick) - bond draw mode
• stick scale (1.0 by default) - scale factor for bonds in the stick draw mode. The stick scale is multiplied by individual bond radii (default 0.2 angstroms) to generate stick radii in angstroms. Changing stick scale is preferable to changing all of the bond radii in a model, because the former will also scale singleton atoms in the endcap draw mode appropriately. Either way, the other endcap atoms (those participating in bonds) will be scaled to match the thickest of the attached bonds.
• ball scale (0.25 by default) - scale factor for atoms in the ball draw mode. The ball scale is multiplied by individual atom VDW radii to generate ball radii in angstroms.
• 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)
• metal complex line width (1.0 by default) - pixel width of pseudobonds depicting metal coordination (when in the wire draw mode)

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 Data Bank web site when it is not found locally (see the Web Access preferences for proxy settings, if needed)
• 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 Preferences section of the Preferences Tool includes:

• Preferences file - 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)
• All categories:
  • Restore to saved settings - replace the current settings in all categories with those previously saved in the preferences file
  • Reset to factory defaults - replace the current settings in all categories with the original defaults
  • Save - save the current settings in all categories to the preferences file

The Tools section of the Preferences Tool allows control over the following Settings for each tool (extension):

• Auto Start - whether to launch the tool automatically upon Chimera startup
• On Toolbar - whether to show the tool's icon in the toolbar
• In Favorites - whether to include the tool in the Favorites menu
• Confirm on Start - whether to ask for confirmation before starting the tool

The Web Access section of the Preferences Tool includes:

• Confirm open of commands or code (once per session/each time/never) - whether/how often to ask for confirmation before opening certain types of data linked to web pages. The default is to ask once per Chimera startup.
• Accept web data (true/false) - whether the running instance of Chimera can be used as a helper application for data linked to web pages (and can receive files specified with chimera --send). On Mac OS X, this preference is not shown, and is effectively always true. After a browser has been configured to send Chimera certain types of files, setting Accept web data to true enables the running instance of Chimera to accept such files. If there is no running instance of Chimera enabled to accept web data, another instance of Chimera will be started and used to open the data. If there are multiple running instances of Chimera set to accept web data, the file will be sent to the instance that most recently had focus (was most recently clicked into).
• Use HTTP proxy (true/false) - whether to use a proxy to connect to the internet through a firewall (for example, to fetch a PDB file from the Protein Data Bank web site); the server and port number settings (below) should generally be the same as those used for web browsers
• Proxy server - the hostname or IP address of the proxy server
• Proxy port - proxy port number to use