The following are options that can be specified when starting Chimera from the system command line. Arguments containing spaces should be enclosed in quotation marks.
Whether to make the background in saved images transparent, if system hardware permits. With this option on, PNG and TIFF images saved from Chimera will include opacity information, making them easier to composite with different backgrounds in image-editing applications; if the Chimera background is a single solid color, it will be completely invisible in the saved images. (Note: TIFF images with background transparency may not be interpreted correctly by Adobe Photoshop.) Background transparency can also be enabled in the Save Image dialog or with the command set bgTransparency. For background transparency in raytraced images, see the POV-Ray Options preferences.
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.
Open Debug Graphics Driver to selectively enable/disable OpenGL features before starting Chimera. This should be used only to find workarounds for graphics driver bugs, because in the absence of such problems, changing the settings from the system defaults is expected to degrade Chimera performance and/or appearance. Showing Debug Graphics Driver at startup can also be specified in the General preferences.
Whether to start in fullscreen mode (available in Windows, Linux, and Mac-X11 versions of Chimera).
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.
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 except for error messages and those produced by print statements. 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 OpenGL multisampling, i.e., multiple samples per pixel so that edges are antialiased. If not well supported by the system, rendering with this option can be very slow or reveal graphics driver bugs. Multisampling can also be controlled in the Effects tool.
Use pref_file (specified with a relative or absolute pathname) as the preferences file for the Chimera session.
Add directory to the front of the Python module search path.
Report the Chimera version and build number (no startup). The --version option is similar but more verbose.
Report the Chimera root directory (no startup).
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.
--script "script.py script-arg1 script-arg2 ..."
Execute the script using the arguments enclosed along with it in quotes. Any data files specified in the startup command are opened before the script is called. For example,
chimera --nogui --nostatus --script "myscript.py -r 1.8 3wrp.pdb" 1jhg.pdb
would open 1jhg.pdb and then execute myscript.py with the arguments -r 1.8 3wrp.pdb. As with the command runscript, the chimera module is pre-imported into the script's global namespace, and the arguments are made into a tuple variable in the global namespace called "arguments" containing however many strings were supplied. The arguments are also available in the standard sys.argv location. For more details, see #3 in the Programmer's FAQ.
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).
Whether to suppress all messages except for error messages and those produced by print statements. Useful for running scripts and for debugging. See also --nostatus.
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.
Whether status messages should be generated when nogui mode is used. See also --silent.
Specify startup camera mode; possible values of mode are the same as for the command stereo: mono (default, not in stereo), sequential, cross-eye, wall-eye, red-cyan, green-magenta, and others.
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 Chimera version and build number (no startup). The --release option is similar but more terse.
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.