Many of the command-line options for Chimera are special-purpose and unlikely to be used very frequently.
--bgopacity
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 images saved from the session will include opacity information, making them easier to composite with different backgrounds in image-editing applications. 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.
--debug
(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. Note that --pypath can be used to add directories to front of the Python module search path.
--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.
--listfiletypes
List the file types that can be read by Chimera and the corresponding filename prefixes and suffixes (no startup).
--nogui
Run Chimera without a graphical user interface. This is useful in combination with Python input that generates output such as text files that need not be viewed with the Chimera graphics window.
--nostencil
(currently undocumented)
--pypath directory
Add directory to the front of the Python module search path.
--root
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.
--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).
--start Tool_name
Launch the tool named Tool_name upon Chimera startup. This option can be used more than once in the command line. Individual tools are documented in the Tools section of the Chimera User's Guide (and after Chimera has been started, the available tools are listed under Tools in the menu. If Tool_name contains any spaces, it must be enclosed in double quotes, for example: "Volume Viewer".
--stereo
Start Chimera in sequential stereo mode. Success of this option is contingent upon the presence of appropriate hardware.
An extra step is needed to remote display in stereo to an SGI.
--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.
--version
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.