Preferences

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

By default, preferences are stored in the file $HOME/.chimera/preferences, where $HOME refers to the user's home directory. The location can be changed in the Preferences section of the Preferences Tool. The preferences file can contain information in addition to the Preferences Tool settings, including the names of recently accessed files and directories.

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.

Background

The Background section of the Preferences Tool includes:

Collaboratory

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.

General

The General section of the Preferences Tool includes:

Image Credits

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.

Image Setup

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.

Messages

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

Midas

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:

and either or both are executed (in the order listed), if found. The defaults can be deleted and/or additional names and locations can be added to the list. The files are treated as if they had been sourced in the Command Line. 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 here after commands unsupported by Chimera have been removed.

Mouse

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 preferences 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.

New Molecules

The New Molecules section of the Preferences Tool controls how newly opened molecules will initially appear:

PDB

The PDB section of the Preferences Tool includes:

Preferences

The Preferences section of the Preferences Tool includes:

Tools

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

The Locations section allows users to specify additional directories for Chimera to look in for tools. Clicking Add opens a dialog for directory specification. Delete removes a directory from the list.

Web Access

The Web Access section of the Preferences Tool includes: