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, 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.

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.

Background

The Background section of the Preferences dialog includes:

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: PDB preferences

General

The General section of the Preferences dialog includes:

In the Mac Aqua 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.

Messages

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

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 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.

iconmeaning default assignment iconmeaning 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.

Some tools create additional mouse modes represented by different icons, 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 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

New Surfaces

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

Tools

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

The 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 / November 2009