System Command-Line Options

The following are options that can be specified when starting Chimera from the system command line.

--nobgopacity (default)

Whether to make the background transparent and allow its opacity to be adjusted (opacity = 1 - transparency). Not all systems have the hardware required to support this option. PNG and TIFF images saved from the session will include opacity information, making them easier to composite with different backgrounds in image-editing applications. (Note: TIFF images with background transparency may not be interpreted correctly by Adobe Photoshop®.) With this option, the opacity is initially set to zero; if the background color is subsequently changed, however, the background will no longer be transparent unless the color definition includes transparency. Background transparency can also be enabled in the Effects tool.
--nodebug (default)

Whether to (1) put the current directory at the front of the Python module search path instead of at the end, and (2) turn off redirection of standard error to the Reply Log. On UNIX, the standard error will go to a terminal window. On Windows, the standard error will go to a separate chimera debug console window, which opens automatically when --debug is used. The --pypath option can be used to add directories to front of the Python module search path.
--nofullscreen (default)

Whether to start in fullscreen mode (Windows only).
--geometry wxh+x+y
Set the size and location of the Chimera window. The variables w and h are the width and height of the window in pixels, and x and y are the X and Y offsets of the top left corner of the window from the top left corner of the screen. The wxh part of the argument can be omitted if size control is not important. The +x+y part of the argument can be omitted if controlled placement is not important. Depending on the system, various borders and menubars may or may not be included, so some experimentation may be required to size and place the window exactly as desired.
--gui (default)

Whether to run Chimera with a graphical user interface. The --nostatus option can be used to suppress status messages when in nogui mode, while --silent can be used to suppress all messages other than print statement outputs. If the last argument in the startup command is not a script file and --script is not used, a prompt will be supplied in the system shell for entering Chimera commands on standard input.
List the file types that can be read by Chimera and the corresponding filename prefixes and suffixes (no startup).

Whether to use use multiple samples per pixel so that edges are antialiased (the default setting depends on the graphics card). Most modern graphics cards support multisampling, although certain graphics driver bugs may necessitate turning it off.
--preferences pref_file
Use pref_file (specified with a relative or absolute pathname) as the preferences file for the Chimera session.
--pypath directory
Add directory to the front of the Python module search path.
Report the Chimera root directory (no startup).
--screen screen_number
Use a particular monitor for display (useful when multiple monitors are hooked up to the computer). The default is 0, usually the only monitor attached.
Put all unprocessed arguments into sys.argv for the script to handle. The end of arguments for Chimera can be indicated with --. For example,
chimera --nogui --nostatus --script -- -p 1jhg -r 1.8
would pass the arguments -p 1jhg -r 1.8 to the script. See the Programmer's FAQ for more details.
--send input
If there is a running instance of Chimera that is set to accept web data, use it to open the file input; otherwise, start a new instance of Chimera to open the file. 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).
--nosilent (default)

Whether to suppress all kinds of messages except those produced by print statements. Useful for running scripts and for debugging. See also --nostatus.
--start Tool_name
Launch the tool named Tool_name. This option can be used more than once in the same startup command. Individual tools are documented in the Tools section of the Chimera User's Guide and listed in the Chimera Tools menu. If Tool_name contains any spaces, it must be enclosed in double quotes, for example: "Volume Viewer". This is just one of several ways to start a tool.
--status (default)

Whether status messages should be generated when nogui mode is used. See also --silent.
--nostereo (default)

Whether to start Chimera in sequential stereo mode. Sequential stereo is a rapid flickering between left-eye and right-eye views; special synchronized glasses are needed to obtain the three-dimensional effect. This mode is not always available.
--title title
Change the title of the Chimera window (shown on the top bar) from the default of Chimera to the string title. If title contains any spaces, it must be enclosed in double quotes.
Report the version of Chimera (no startup).
--visual visual_id
Use a different visual setting than that determined automatically by Chimera (does not apply to Windows; on other systems, visual ID numbers and properties can generally be listed by commands such as glxinfo, xglinfo, or xdpyinfo). This option is mainly for debugging rather than general usage.

UCSF Computer Graphics Laboratory / June 2008