A Chimera preferences file contains settings from the Preferences dialog and additional information such as recently accessed files and directories.

A particular preferences file can be specified with --preferences at startup. Otherwise, Chimera will look for a file named preferences first in the current directory, then in a .chimera subdirectory of the current directory, then in the .chimera subdirectory of the user's home directory. On Windows, what is considered the home directory in this context depends on a user's profile, but is often C:\Documents and Settings\username\Application Data\. The file location is reported in the Preferences preferences. Preference changes and other information from the current session will be saved to this file unless it has been designated read-only.

This system allows a user to maintain a single set of preferences for all Chimera sessions, or different preferences specific to data in different directories, or a combination of these.

If no preferences file is found, Chimera will look for a writable location for a new preferences file in the following order: the user's home directory (a subdirectory .chimera with a preferences file within it will be created), a subdirectory .chimera of the current directory, the current directory. If none of these directories are writable, an error message will appear.

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

• Animation
• Background
• Command Line
• Fetch
• General
• Image Credits
• Messages
• Mouse
• Movie
• New Molecules
• New Surfaces
• PDB
• POV-Ray Options
• Preferences
• Tools
• Web Access

Help opens this manual page in a browser window, and Close dismisses the Preferences dialog.

Default settings are indicated below in bold.

The Animation section of the Preferences dialog includes settings for scenes and the Animation tool. See also: Movie preferences, scene

• Scene name prefix (default sc)
• Scene thumbnail size (default 60 pixels) - width and height of scene thumbnails in the Animation and Rapid Access interfaces
• Transition name prefix (default tr)
• Show orphan dialog (true/false) - whether to show a warning and allow cancellation when the user attempts to close a model that is included in a saved scene

The Background section of the Preferences dialog includes settings for the graphics window background, labels, and selection highlighting. See also: background

• Background method (solid/gradient/image) - whether the background should be a single solid color (default), a gradient of multiple colors, or an image
• Background color (a color well, default No Color, equivalent to black) - color to use when the background method is solid
• Background gradient (a palette well, default HLS-interpolated white to blue) - palette to use when the background method is gradient; left-to-right order in the palette well corresponds to bottom-to-top order in the graphics window
  • opacity (default 1.0) - gradient opacity, ranging from 0.0 (completely transparent) to 1.0 (completely opaque); transparency reveals the current solid background color. If a transparent gradient is used at the same time as the transparent background option in Effects, the background of an image saved from Chimera as PNG or TIFF will not only show the blending of the gradient over the solid color, but also have the same overall opacity as was specified for the gradient.
• Background image (an image well, default No image) - image to use when the background method is image; clicking the well brings up a file browser for locating and opening an image file, where accepted formats include PNG, TIFF, and JPEG. The image can be fit into the graphics window in any of the following ways:
  • zoomed (default) - automatically scaled to fill the window, top/bottom or sides cropped as needed (no image distortion)
  • stretched - automatically scaled to fill the window, stretched or squashed as needed
  • centered - centered with any surrounding border shown in the current solid background color
  • tiled - tiled to fill the window
  Additional image settings:
  • scale (default 1.0) - image scale factor, applies only when the image is centered or tiled
  • opacity (default 1.0) - image opacity, ranging from 0.0 (completely transparent) to 1.0 (completely opaque); transparency reveals the current solid background color. If a transparent background image is used at the same time as the transparent background option in Effects, the background of an image saved from Chimera as PNG or TIFF will not only show the blending of the background image over the solid color, but also have the same overall opacity as was specified for the background image.
• Label font (Sans Serif/Serif/Fixed) (Normal/Bold/Italic/Bold Italic) (6/8/9/10/11/12/16/18/24/30/36) - font typeface, style, and size to use for 3D labels
• Labels on top (true/false) - whether to draw 3D labels in front regardless of their Z-offsets
• 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

The Command Line section of the Preferences dialog is only available after the Command Line has been shown.

• Files to read at startup - what command files, if any, should be opened when the Command Line is started. There are two defaults:
  • $HOME/.chimera/midasrc (in a subdirectory named .chimera of the user's home directory; on Windows, what is considered the home directory in this context depends on a user's profile, but is often C:\Documents and Settings\username\Application Data\)
  • .chmidasrc in the current directory
  and either or both are executed (in the order listed), if found. Files can be added to or deleted from the list. Whether files are listed by name followed by path or with the path preceding the name is controlled in the General preferences.

  Startup files are especially useful for defining aliases and color names.

• Number of commands to remember between sessions (default 60) - length of command history to save to the preferences file when exiting from Chimera; the saved commands will be shown in the Command History in the next session that uses the same preferences file.

The Fetch section of the Preferences dialog controls handling of data retrieved over the Web from various databases. See also: PDB preferences, Fetch by ID

• Save fetched files (true/false) - whether to save fetched files locally; even if this option is true, no files will be saved unless a download directory has also been specified
• Use local files (true/false) - whether to look in the download directory and use a previously fetched copy (if any) when Fetch by ID or the open command is used to fetch a file from a database; when true, can be overruled by using the Fetch by ID option to Ignore any cached data
• Download directory (default ~/Downloads/Chimera) - where to store fetched files locally; subdirectories for the different databases will be created as needed. On Windows XP, the default is ~/My Documents/Downloads. If the specified location does not exist, fetched files will not be cached.

The General section of the Preferences dialog includes:

• Confirm exit (true/false) - whether to ask for confirmation before exiting Chimera when File... Quit has been chosen or the command stop has been entered (does not apply to occurrences of stop in command files)
• 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) - when the cursor is paused over an object (atom, bond, surface, etc.), whether to show the corresponding label information in a balloon in the graphics window, and PDB chain information, if available, in the status line. The number of decimal places shown for bond distances can be set with the Distances tool.
• Atomspec display style (simple/command-line specifier/serial number) - how to list atoms in atomspec balloons, Structure Measurements, and Metal Geometry. Atom naming styles:
  • simple - residue name, residue specifier, and atom name (for example, HIS 16.A ND1)
  • command-line specifier - a specification string that could be used in the Command Line (for example, :16.A@ND1)
  • serial number - atom serial number (for example, 126)
  Model number (for example, #0) will also be included when multiple models are present.
• 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 Command Line preferences); a change will not be evident until after Chimera is restarted
• Fullscreen graphics (true/false) - whether the graphics window is in fullscreen mode (Windows only)
• Try to avoid placing dialogs over main window (true/false) - whether to try to place additional Chimera dialogs alongside the graphics window instead of on top of it
• File browser confirms overwrite (true/false) - whether to ask for confirmation before overwriting a file with a save dialog
• 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.
• Debug OpenGL on startup (true/false) - whether to open Debug Graphics Driver at startup to selectively enable/disable OpenGL features before starting Chimera. This should be used only to find workarounds for graphics driver bugs, because in the absence of such problems, changing the settings from the system defaults is expected to degrade Chimera performance and/or appearance. Debug Graphics Driver can also be called with the startup option --debug-opengl.
• Update check interval (never/daily/weekly/biweekly/monthly/quarterly) - how often to check whether a newer version of Chimera (snapshot or production release) is available
• Initial window size (remember last/fixed) - how to determine the size of the window at startup
• Fixed size - pixel width and height for fixed initial window size

• Menus in windows on Mac (true/false) - whether to show Chimera menus in-window as well as across the top of the screen

The Image Credits section of the Preferences dialog 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 Messages section of the Preferences dialog 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

Mouse button functions including the manipulation of models can be reassigned using the Mouse section of the Preferences dialog. Functions may be assigned to the left, middle, and right mouse buttons alone and in combination with the Ctrl key. There can be no more than one function checked per row (per button or Ctrl-button). Mice with fewer than three buttons can be accommodated.

icon	meaning	default assignment		icon	meaning	default assignment
	rotation	1 (left button)			picking (selection from screen)	Ctrl-1
	XY-translation	2 (middle button)			Z-translation	Ctrl-2
	scaling	3 (right button)			label-dragging (XY, +Shift for Z)	Ctrl-3
	pop-up Chimera menu	(none) see alternatives

Continue rotation after mousing (true/false) indicates whether rotation should continue when the corresponding mouse button is released while the cursor is in motion.

Use mouse scroll wheel (true/false) indicates whether the mouse scroll wheel and touchpad scrolling should also scale the view.

Some tools create additional mouse modes represented by different icons, for example:

tool	icon	meaning
Adjust Torsions		bond rotation
2D Labels		2D label placement
Color Key		color key placement

The Movie section of the Preferences dialog includes settings for recording movies. See also: Animation preferences

• Image format (jpeg/png/ppm) - image file format (however, png format will be used for raytraced images regardless of this setting)
• Image supersampling (none/on-screen/2x2/3x3/4x4) - supersampling refers to generating an initial image larger than the window and sampling it down to the final size. This increases the smoothness of edges within images and the calculation time without affecting file size. A level of 3x3 is recommended if supersampling is done. Rendering is normally off-screen, but on-screen rendering (without supersampling) can be specified.
• Movie format
  • MPEG-1 [.mpg]
  • MPEG-2 [.mpg]
  • MPEG-4 [.mp4]
  • AVI MSMPEG-4v2 [.avi]
  • Quicktime [.mov] (default)
• Playback bit rate (variable/constant) - whether the movie should be encoded to play back at a constant or variable data rate. At a given window size and frame rate, higher bit rates (whether constant or variable) give better movie quality but also larger files. Increasing the window size and/or frame rate without increasing the bit rate decreases movie quality.
• Quality (variable bit rate) (8) - quality factor for variable-rate playback, ranging from 1 (highest quality and highest rates) to 31 (lowest)
• Constant bit rate (2000) - constant rate in Kbits/s; generally, 200 is low quality, 1000 medium, and 6000 high
• Frames per second (25) - image frames per second during playback
• Buffer size (Kbytes) (0)
• Reset mode (clear/keep/none) - after movie encoding, whether to reset the frame counter to 0 and clear (delete) the images, or reset and keep the images, or none (neither reset nor remove images). Clicking Reset in the Movie Recorder dialog will always reset the counter, but will not change the image filename pattern automatically if this setting is none.

The New Molecules section of the Preferences dialog controls how newly opened molecules will initially appear. New Molecules settings can be circumvented by opening structures with the command open noprefs; this prevents inconsistent behavior of command files and demos potentially caused by the different preferences settings of different users. See also: molecule model attributes, presets

• 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 setting can also be controlled with set/~set autocolor. If the solid background color is black or white, automatic model colors are 0:tan, 1:sky blue, 2:plum, 3:light green, 4:salmon, 5:light gray, 6:deep pink, 7:gold, 8:dodger blue and 9:purple (see named colors). Thereafter, or for all models if the solid background color is not black or white, an algorithm is used to produce colors distinguishable from the background and from other models.
• otherwise, use color (a color well, by default a light gray) - model-level color if not using a new color for each model
• smart initial display (true/false) - show newly opened molecule models with settings similar to the ribbons preset, but without rainbow-coloring chains or altering global parameters such as background color. Smart initial display overrides other New Molecules preferences except for those affecting initial model color, line width, stick scale, ball scale, metal complexes, and Mol2 model naming.
• ribbon display (off/on) - whether to show ribbon; ribbons are only drawn for proteins and nucleic acids. Protein helix and strand assignments are taken from the input structure file or generated with ksdssp.
• ribbon cross section (edged/flat/rounded/any additional styles created and named with the Ribbon Style Editor) - ribbon style (see also ribrepr)
• ribbon scaling (Chimera default/licorice/any additional scalings created and named with the Ribbon Style Editor) - ribbon scaling (see also ribscale)
• 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 (excluding monatomic ions)
• bond style (wire/stick) - bond draw mode
• monatomic ion style (dot/ball/endcap/sphere) - draw mode to use for monatomic ions
• 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.
• per-atom coloring (none/by element/by heteroatom) - whether to leave atom colors unassigned (none; atoms will inherit model colors) or to assign element colors to all atoms (by element) or only the non-carbon atoms (by heteroatom)
• auto-chaining (off/on) - whether to connect atoms that precede and follow undisplayed segments (whether to draw pseudobonds between them)
• metal complex line width (2.0 by default) - pixel width of pseudobonds depicting metal coordination (when in the wire draw mode)
• metal complex color (a color well, medium purple by default) - color to use for pseudobonds depicting metal coordination
• dash metal complex lines (true/false) - whether the pseudobonds depicting metal coordination should be shown as dashed (rather than solid) lines when in the wire draw mode
• Mol2 model naming (file name/Mol2 molecule name/Mol2 molecule comment) - how to name models read from Mol2 format: by file name, by molecule name given within the file (on the line below @<TRIPOS>MOLECULE), or by comment text (the sixth line below @<TRIPOS>MOLECULE)

The New Surfaces section of the Preferences dialog sets parameters for newly created molecular surfaces. See also: molecular surface attributes, presets

• representation (solid/mesh/dots) - display type
• probe radius (1.4) - radius in Å of the probe sphere used to compute the surface. A larger probe decreases surface bumpiness because it fits into fewer crevices. A radius of 1.4 Å is commonly used to approximate a water molecule.
• vertex density (2.0) - vertices per Ų. Greater density results in a smoother surface but increases computational demands for calculating and moving the surface.
• line width (1.0) - pixel width of lines used in the mesh surface representation
• dot size (1.0) - pixel size of dots used in the dot surface representation
• show disjoint surfaces (true/false) - whether to check for multiple disconnected parts of a surface (components) rather than assuming there is only one; increases calculation time

The PDB section of the Preferences dialog includes:

• Fetch from web as necessary (true/false) - whether to retrieve a file specified by PDB ID from the Protein Data Bank web site when it is not found locally (see the Web Access preferences for proxy settings, if needed). Chimera first looks for a local installation of the Protein Data Bank, then in any personal PDB directories, and then in the fetch download directory (unless disallowed in the Fetch preferences) before resorting to a Web fetch. The default places to look for a local installation are /usr/mol/pdb/ and then /mol/pdb/ — these can be changed by editing the Python file share/chimera/pdbDir within a Chimera installation.
• Personal PDB directories - additional directories in which to look for PDB files. Directories can be added to or deleted from the list. The directory structure can be flat, where a single directory contains files named xxxx.pdb (and xxxx is the PDB ID), or hierarchical, with pathnames of the form xy/pdb1xyz.ent, where 1xyz is the PDB ID and subdirectory names are the two middle characters of the IDs. PDB filenames of the form pdb1xyz.ent can also be used in the flat directory structure.

The POV-Ray Options section of the Preferences dialog sets specifications for raytracing with POV-Ray.

• POV-Ray executable [ location ] - the location of the POV-Ray executable. This is filled in automatically for the executable included with Chimera, but another location could be specified.
• Show preview (true/false) - whether to show a preview; regardless of this setting, however, a preview will not be shown during movie recording or when Chimera is in nogui mode.
• Quality (default 9, range 0-11) - output image quality, adjusted by omitting calculations that are normally performed. For example, values < 4 yield images without shadows [quality details at the POV-Ray site].
• Antialias (true/false) - whether multiple samples should be averaged to produce a single output pixel; otherwise, POV-Ray will simply trace one ray per pixel. Analogous to (but independent of) Chimera image supersampling, this supersampling in POV-Ray smooths edges in output images [antialias details at the POV-Ray site].
• Antialias method (fixed/recursive) - how pixels should be supersampled when antialiasing is used. In the fixed method, POV-Ray initially traces one ray per pixel. Each pixel is compared to its neighbors to the left and above. If the colors of two pixels differ by more than the antialias threshold, each of the pixels will be subsampled according to the antialias depth (if the depth is 3, a grid of 3*3=9 samples will be taken per output pixel). In the recursive method, POV-Ray initially traces 4 rays at the corners of each pixel. Where the colors of adjacent samples differ by more than the threshold, subsamples will be taken and compared. This process is repeated until adjacent colors agree within the threshold, or the maximum number of subdivision cycles (the specified antialias depth) has been performed.
• Antialias depth (default 3, range 1-9) - meaning depends on which antialias method is used
• Antialias threshold (default 1.0, range 0.0-3.0) - two colors are compared by summing the absolute differences in their red, green, and blue components; differences greater than the threshold trigger further sampling when antialiasing is used. Lower threshold values increase the number of samples and the calculation time, whereas a threshold of 3.0 will suppress further sampling.
• Jitter (true/false) - whether to introduce noise by randomly wiggling the supersample locations when antialiasing is used; not recommended for movie recording, as the random noise will make pixels vary and flicker from frame to frame [jitter details at the POV-Ray site]
• Jitter amount (default 0.5) - values are specified relative to 1.0, which is the most jitter that can be performed while retaining supersamples within the original pixel
• Transparent background (true/false/same as chimera) - whether to make the background transparent by including transparency (alpha) values for output pixels [output alpha details at the POV-Ray site]. The same as chimera option means to follow the current transparent background setting in the Effects tool. It is also necessary to turn off depth-cueing to obtain background transparency in raytraced images.
• Wait for POV-Ray to finish (true/false) - whether to prevent further commands from executing until POV-Ray has finished generating the image. During movie recording, the behavior will always be as if this were set to true.
• Keep POV-Ray input files (true/false) - whether the POV-Ray input files containing the scene (*.pov) and raytracing options (*.ini) should be kept or deleted after the image has been rendered

The Preferences section of the Preferences dialog includes:

• Preferences file - the location of the preferences file for the current session
• Read-only - whether the preferences file for the current session should be treated as read-only. The initial setting reflects the file permissions at Chimera startup. When Read-only is false, Chimera may update the file with changes in preference settings and other information; switching to true prevents subsequent changes in the file. When Read-only is true, Chimera will not update the file; switching to false (if the file is already writable, or is owned by the user) will enable its modification by Chimera.
• 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 dialog allows control over the following Settings for each entry in the Tools menu:

• Auto Start - whether to launch the tool automatically upon Chimera startup
• On Toolbar - whether to include the tool 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

• Toolbar placement (left/right/top/bottom/Rapid Access) - whether to put the toolbar along one side of the Chimera graphics window, or only in the Rapid Access interface

The Web Access section of the Preferences dialog 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.
• 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, this preference is not shown, but is effectively true unless Chimera was started from the terminal command line. A browser must be configured to send the files to Chimera. 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