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, the user's home directory 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:

General

The General section of the Preferences dialog includes:

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.

Midas

The Midas section of the Preferences dialog is only available after the Command Line (formerly known as the Midas Emulator) has been shown.

Files to read at startup refers to what command files, if any, should be sourced when the Command Line is started. There are two defaults:

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.

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 in Chimera after minor adjustments. The differences in atom specification mainly reflect additions, but note that in Chimera, chain IDs are specified differently and mainchain is not accepted as a specifier. A few Midas/MidasPlus commands are unsupported by Chimera.

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)
lens control 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.

New Molecules

The New Molecules section of the Preferences dialog controls how newly opened molecules will initially appear. 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 / March 2008