ChimeraX Startup

The ChimeraX application runs on Microsoft Windows, Apple Mac OS X, and Linux.

By default, ChimeraX does an asynchronous network query of the ChimeraX Toolshed for available bundles at startup once a week. The interval can be changed in the Toolshed settings. The Toolshed query is implicitly turned off when certain command line arguments are given as noted below.

Command Line Arguments

When running ChimeraX from a terminal, a.k.a., a shell, it can be given various options followed by data files. The data files are specified with same syntax as the filename argument of Models’ open().

Command line options can start with either a single dash or a double dash and may not be mixed.

Single Dash Commmand Line Options

All of the Python single dash command line options are recognized. The presence of any single dash argument turns off querying the Toolshed at startup. Most are ignored except for the following:

-c command

Only recognized if it is the first argument. Act like the Python interpreter and run the Python command with the rest of the arguments in sys.argv. Implies --nogui and --silent. This is done after ChimeraX has started up, so a ChimeraX session is available in the global variable session.

-d

Turn on debugging.

-h

Show command line help.

-m module

Only recognized if it is the first argument. Act like the Python interpreter and run the module as the main module and the rest of the arguments are in sys.argv. Implies --nogui and --silent. This is done after ChimeraX has started up, so a ChimeraX session is available in the global variable session. The module name is __main__ instead of a sandbox name that is used for normal scripting.

-u

Force the stdout and stderr streams to be unbuffered.

-V

Prints the internal Python version and exits.

Double Dash Command Line Options

The follow command line arguments are recognized:

--cmd command

Run the ChimeraX command at startup after starting tools. Turns off querying the Toolshed at startup.

--color

Turn on colored text in nogui mode (default).

--nocolor

Turn off colored text in nogui mode.

--debug

Turn on debugging code. Accessing within ChimeraX with session.debug.

--devel

Turn on development mode. Currently, just enables Python deprecation warnings.

--exit

Exit immediately after processing command line arguments. Turns off querying the Toolshed at startup.

--noexit

Do not exit after processing command line arguments (default). Turns off querying the Toolshed at startup (not default).

--lineprofile

Turn on line profiling. See Line Profiling for details. Turns off querying the Toolshed at startup.

--listioformats

Show all recognized file suffixes and if they can be opened or saved. Turns off querying the Toolshed at startup.

--nogui

Turn off the gui. Access with ChimeraX with session.ui.is_gui.

--nostatus

Don’t output to status line.

--notools

Do not autostart any tools at startup.

--offscreen

Run without a gui but allow rendering images that can be saved to files, i.e., implies --nogui. This uses OSMesa for rendering which will not make use of a GPU, so rendering can be slow. But it can run on a server without a display.

--safemode

Don’t run bundle custom initialization code nor load any tools.

--script python-script

Run Python script at startup. If they Python script has any specific arguments, they should be quoted along with the script name. Turns off querying the Toolshed at startup.

--silent

Don’t output startup splash text and otherwise refrain from being verbose.

--start_tool tool_name

Start the named tool during ChimeraX startup after the autostart tools.

--tools

Run ChimeraX tools at startup (default).

--notools

Don’t run ChimeraX tools at startup.

--toolshed URL

Set the URL to use for the toolshed. The special name preview is recognized for using a preview of the next revision of the toolshed (currently only available internally).

--uninstall

If needed, deregister any icons or mime types, then remove as much of the installation directory as possible. Intended for use by system App Store or package manager.

--usedefaults

Ignore user settings and use default settings. Not implemented yet.

--version

Print out current version. If given two times, then all of installed ChimeraX tools verions are listed. If given three times, then all of installed Python package versions are listed.

Run Custom Python Code at Start Up

To have ChimeraX run custom Python code each time you start it you can put Python files in directory

~/chimerax_start

Each Python file will be executed with the variable “session” added to the global namespace. For example, the following line put in ~/chimerax_start/starttools.py automatically starts the File History panel and Density Map toolbar.

session.tools.start_tools((‘File History’, ‘Density Map Toolbar’))

Python code can be used to register new commands, add mouse modes and file readers that you develop. In addition to executing Python files in the directory, the startup directory will be appended to the Python sys.path search path so Python modules in the subdirectory can be imported. Subdirectories in the startup directory that contain an __init__.py file will be imported and if they contain a function named “start” it will be called with session as an argument.

To use a directory other than ~/chimerax_start as the startup directory set the environment variable CHIMERAX_START to the desired directory in the shell where Chimera is started.

Initializing the Session

A Session instance is passed as an argument to many functions. It is the way to access per-session data. Leaf functions frequently are only given one attribute (or none at all).

session.debug

True if debugging.

session.logger

A Log instance to log errors to.

session.app_dirs

A versioned AppDirs instance with directories to look for application and user files in.

session.app_dirs_unversioned

An unversioned AppDirs instance with directories to look for application and user files in.

session.app_data_dir

The location of “share” directory.

session.ui

A Log instance.

session.toolshed

A Toolshed instance.

session.tools

A Tools instance.

session.tasks

A Tasks instance.

Other initial sessiona attributes are initialized in chimerax.core.session.common_startup().

Line Profiling

Line profiling is based on Robert Kern’s line_profiler package. Support is restricted to platforms that have binaries in pypi.org (just Linux for now). Differences from the conventional setup are given in parenthesizes.

There are five parts to profiling:

  1. Decorate functions that you wish to profile with the @line_profile decorator and install them. This decorator is a no-op if ChimeraX is not profiled. (Instead of the conventional @profile.)

  2. Run ChimeraX --lineprofile from the command line. (Instead of using kernprof.) This generates a ChimeraX.lprof file in the current directory.

  3. Get your profiling results by running ChimeraX -m line_profiler ChimeraX.lprof.

  4. Analyze your results, possibly edit your code, and return to step 1.

  5. Remove the function decorators before committing your changes.

To use the timeit module, see the scripting documentation.