Preferences File

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 (the startup location, unless cd has been used), if not found then in a .chimera subdirectory of the current directory, and if not found in either of those places, then:

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.

Preferences Dialog

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

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 in the Preferences section of the Preferences dialog.

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

Default settings are indicated below in bold.

Animation

The Animation section of the Preferences dialog is only available after a scene has been saved or the Animation tool started. See also: scene

Background

The Background section of the Preferences dialog includes settings for the graphics window background. See also: background

Command Line

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

Fetch

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

General

The General section of the Preferences dialog includes:

In the Mac version of Chimera only:

Image Credits

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.

Labels

The Labels section of the Preferences dialog contains settings for 3D labels (those which move along with the structure) and pop-up atomspec balloons. The method of residue label positioning can be set in the molecule model attributes panel or with the command setattr. See also: 2D Labels

Messages

The Messages section of the Preferences dialog controls the disposition of various messages and whether balloon help is shown.

Mouse

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. (Modifier keys allow accessing these functions with a touchpad or simpler mouse.) There can be no more than one function checked per row (per button or Ctrl-button).

iconmeaning default assignment
rotation 1
(left button)
XY-translation 2
(middle button)
scaling 3
(right button)
       picking
(selection from screen)
Ctrl-1
Z-translation Ctrl-2
 click item (atom, bond, surface vertex...)
to center, set as fixed center of rotation;
click empty space to restore
front center mode
Ctrl-3
pop-up Chimera menu (none)
see alternatives
label-dragging
(XY, +Shift for Z)
(none)
In the Mac version of Chimera only:

Some tools create additional mouse modes, for example:

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

New Molecules

The New Molecules section of the Preferences dialog controls how subsequently opened molecule models 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 different preference settings of different users. By default, these preferences are not applied to structures opened via Chimera web data (chimerax) files, but noprefs="false" can be set in the chimerax file to indicate that the preferences should be applied. Regardless of noprefs options, however, the preferences for metal complex depiction and mol2 naming are always applied. See also: open, molecule model attributes, presets

New Surfaces

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

PDB

The PDB section of the Preferences dialog includes:

POV-Ray Options

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

Preferences

The Preferences section of the Preferences dialog includes:

Presets

The Presets section of the Preferences dialog allows specifying Personal preset directories in which Chimera should look for custom preset scripts. Directories can be added to or deleted from the list. Preset script file types:

Custom presets will appear in the Presets menu in alphabetical order by name, which is determined from script filename: name.preset.suffix where suffix indicates the file type, as listed above. In other words, the filename must end in “.preset.com,” “.preset.cmd,” or “.preset.py.” Custom presets can also be accessed with the preset command.

Selection

The Selection section of the Preferences dialog controls how selections are highlighted.

Tools

The Tools section of the Preferences dialog allows control over the following Settings for each entry in the Tools menu:

The toolbar is shown when it includes at least one icon. The Third-party plugin locations section allows users to specify additional directories in which Chimera should look for tools. Directories can be added to or deleted from the list.

Web Access

The Web Access section of the Preferences dialog includes:


UCSF Computer Graphics Laboratory / May 2021